Migrating to a new Shopify store, and you sell supplements. Migrate everything to a new Shopify store.
You are moving to a new Shopify account — whether because a payment processor cut you off, you are restructuring your business, or you simply need a fresh start. The email to yourself feels straightforward: export the old store, import into the new one, done. Here is what actually happens. Shopify's own CSV export cannot carry metafields, metaobjects, orders, gift card codes, videos, themes, menus, discounts or redirects. Those things exist in your store right now. They will not come with you on their own. Even when data does move, reference-type metafields copied naively will still point at objects in the old store, so pages render with sections silently empty — your customer sees a broken layout and you do not know why. This is not a failure of process. It is the real shape of the problem. The only way through is to move deliberately, then run the whole migration a second time and compare counts — products, orders, customers, redirects, all of it — so you know what is actually missing before you flip the switch.
Move all of it into a new store, from $247
One-time packages, no per-record metering, no quotes. The order form unlocks the moment you pay, counts are matched against your old store, and the entire migration then runs a second time — the second pass has to create nothing.
What you are looking at
- CSV export sits in your email, but it contains only SKUs, prices, handles and text fields — no images, no metafields, no order history, no discounts
- The new store builds, products look half-finished, and redirects are gone so search traffic drops immediately
- Gift card codes you issued do not appear anywhere, and no one can tell you how to get them back
- Reference metafields that pointed to collections or pages now point at nothing, leaving theme sections blank
- Custom menus you spent hours building are not there, so navigation is broken
The real urgency is data loss, not speed. A reference-type metafield pointing at the old store will stay broken once you flip traffic to the new one, and by then fixing it means downtime. The genuine deadline is the period before you go live — you must validate everything works while you still have both stores running and can check the old one. After cutover, the old store is usually deleted and there is no way back.
Why it happened — specifically for supplements
Shopify Payments is underwritten by Stripe, which allows supplements but prohibits those that are 'not safe or make harmful claims'. The primary trigger is disease claims: anything stating or implying your product treats, prevents or cures a condition reads as marketing an unapproved drug. The secondary trigger is subscription refund disputes — when a customer cancels because the product 'did not work', the chargeback rate can spike, which is why free-trial-to-subscription models are a specific, well-documented decline reason across acquirers.
Rule out the easy fix first — then deal with the real one
Rule this out first. Shopify does not document a platform route for supplements — there is no attestation or pre-approval gateway. What merchants try first is connecting Shopify Payments and hoping the underwriting review misses the claims. It usually does not. If you are reading this, that review has already declined you. The honest move is to find an acquirer who specializes in ingestible categories and whose underwriting is built around the claims audit, not a blanket refusal. That is not faster, but it is the actual path.
It only helps if all of these are true:
- Your product descriptions contain no disease claims — only structure and function language.
- You use payment methods other than free trial to subscription, or you accept a higher chargeback reserve.
- Your current processing history shows a chargeback rate below the acquirer's stated threshold.
- You have documented supplier credentials and, where applicable, third-party testing results.
If any one of them does not hold, you are where everyone else on this page is: you need a store built around a gateway that will actually accept you — and everything you have built has to move into it without losing the catalog, the customers, the order history or the rankings.
What this means for a business like yours
💊 Sold to be swallowed, inhaled or applied — health claims and product-liability risk
Your product pages carry compliance weight they don't carry for other merchants. A claim on the old store—'supports', 'promotes', 'helps'—gets copied to the new one as written, and if it crosses into drug claim territory, it travels with you. Before migration, have the claims language reviewed by someone who reads them the way a regulator does. Also audit your certificates of analysis, test reports, and allergen disclosures: they need to be linked where a customer can find them in ten seconds, not buried in a PDF folder. A new store is the moment to get this clean, because your dispute rate—the 'it didn't work' chargebacks that plague consumables—will reflect whatever pages you land with. Take the time to separate marketing from claims before you move.
🔁 Recurring billing is a large share of revenue
A subscription business cannot afford downtime on stored payment methods. Your subscriber base and their billing schedules live in Shopify, and they will move with the store, but their payment method tokens are held by your processor, not by Shopify, and cannot be exported or imported at all. This means every subscriber's next billing date arrives at the exact moment you are most likely to have connectivity problems or incomplete migration. If you use Shopify Payments, tokens stay with Shopify—your new store can access them immediately. If you use a third-party processor, confirm in writing that they will release or continue to serve payment methods without interruption during the cutover window. Plan the migration for a day after your heaviest billing cycle, and notify subscribers 48 hours in advance that billing may be delayed. A lost billing cycle is revenue you will never recover.
📦 Thousands of SKUs, deep variant matrices, distributor feeds
Your metafields and metaobjects do not travel in Shopify's CSV export, which means any custom data—size matrices, distributor stock levels, compliance tags, pricing rules—either gets rebuilt by hand or gets lost. For a catalog of thousands of SKUs, hand-rebuild is impossible. You need a migration tool or script that can read your metafield schema from the old store and write it to the new one, field by field. Also watch for reference-type metafields that point to other products or collections: if they are copied naively, they still point at objects in the old store, so pages render with sections silently empty. Your distributor feeds—if they push data to product fields—will also break during migration because the feed is configured against the old store's API endpoints. Before you migrate, audit which custom fields are reference-type and which are populated by external feeds, then arrange for those to be re-pointed or rebuilt on day one. A catalog-heavy store that loses reference resolution looks live but serves broken pages.
What you actually have to fix
Underwriters do not change their minds because you asked. They change them because the facts changed. For supplements, these are the facts that move the decision:
Remove or rewrite every disease claim on your store
This is the single highest-yield fix. Anything that says or implies your product treats, prevents or cures a condition — anxiety, pain, sleep, inflammation, immunity — reads to an underwriter as a drug claim, which moves you from restricted to prohibited. Audit your product descriptions, your blog, customer reviews you display, your email flows and your FAQs. Reframe in terms of structure and function: 'supports joint health' instead of 'cures arthritis', 'promotes relaxation' instead of 'treats anxiety'. Check every claim against FDA guidance on dietary supplements.
Get product liability insurance and verify coverage for ingestibles
Most acquirers will not move forward without a current certificate. This is not optional. The policy must cover your specific product type — protein powders, botanical extracts, sports nutrition — and the certificate should state that clearly. Email your broker or insurer to confirm coverage for the formulations you actually sell. When you apply, provide the certificate with effective dates and policy limits visible. Underwriters will call to verify it before they approve anything.
Document your supplier chain and testing for every product SKU
Acquirers ask for formulation sheets, ingredient sourcing, and either third-party testing results or cGMP certification from your manufacturer. This matters especially if you use botanical extracts, proprietary blends or anything that requires batch verification. Organize this by SKU and have it ready to upload with your application. If you do not have it, ask your supplier for it now. A missing COA or sourcing sheet often stalls an underwriting review for weeks.
Fix your subscription billing model if you use free trials
Free trial followed by automatic subscription is a known chargeback trigger — customers cancel late and dispute the first paid charge. If you use this model, you have two options: switch to paid trial or add a charge-delay period with clear confirmation language before the first payment. Acquirers will ask about your cancellation rate and your refund process. Lower the friction to cancel and you lower the dispute rate, which makes underwriting easier. Disclose your actual chargeback percentage upfront when you apply.
What underwriting will ask you for
- Product liability insurance certificate (required for all ingestible categories and the single most common request).
- Complete product formulations and ingredient sourcing documentation.
- Copies of all marketing claims — product pages, email flows, social media and reviews displayed on your store.
- Testing certificates or cGMP documentation for manufactured products.
- Chargeback and refund history from your current processor for the past 12 months.
- Subscription terms and cancellation rates if you use recurring billing.
Getting underwritten for supplements
High-risk acquiring is an entire industry that exists for businesses Stripe declines, and several of them publicly underwrite supplements. What none of them will tell you up front is the number that actually matters: what your business gets offered, once they have seen your volume, your claims and your history. Rate, reserve and settlement terms vary enormously between applicants in the same category.
Get real quotes from high-risk processors that accept supplements
Six taps and three details. We put it in front of the high-risk acquirers that actually underwrite your category and come back with what they will offer you — rate, reserve and settlement terms — so you are comparing real numbers instead of cold-emailing brokers for a fortnight.
The recovery playbook
- Audit what your store actually containsList everything that matters: products, orders, customers, discounts, redirects, gift cards, navigation menus, theme choice, metafields and metaobjects. Do not assume you know. Log into your current store and count. Orders and gift card codes will not export through CSV — you will need those lists for manual verification later. Make a spreadsheet with baseline numbers for every category. This is the document you will compare against in step 5.
- Get a verified copy of your store out while you still have access — todayBefore you create the new account, request a full backup from Shopify support in case something goes wrong. This is the step people skip, and it is the only one with a deadline you do not control. A migration is not an instant thing — it can take days or weeks, and you will still have the old store running. But the moment you delete it, a full backup becomes impossible. If a metafield is misconfigured in the new store, or a theme does not carry over, or reference data points nowhere, you may need to look at the old store to understand why. Once it is gone, that information is gone. Backups are the only insurance you have.
- Export and move what CSV can carry, manually handle what it cannotRun Shopify's CSV export. It will contain products, variants, prices, handles and text fields. It will not contain metafields, metaobjects, orders, gift card codes, videos, themes, navigation menus, discounts or redirects. Move the CSV into the new store. Then handle the missing categories one by one: metafields must be recreated (some third-party apps can help, but none are universal); orders must be exported from reports as a separate archive; gift card codes cannot be read through any Shopify API and must be re-issued; videos and media must be re-uploaded; themes must be selected and configured again; navigation menus must be rebuilt; discounts must be recreated; redirects must be re-entered or exported from a third-party SEO app if you used one.
- Check reference metafields point to the new store, not the old oneIf you use reference-type metafields — fields that link to collections, pages, products or other objects — those references will still point at the old store after migration. Pages will render with sections blank or broken. You must systematically update each reference to point at the equivalent object in the new store. If a metafield references a collection called 'Summer Dresses', find that collection in the new store and re-link it. This is tedious. There is no way around it. Skipping it is why new stores launch with invisible sections.
- Run the migration again, count everything, and compareBefore you go live, treat this as a full second migration. Export the old store's data again. Import it into the new store again, overwriting what is there, so you capture any changes made in the old store since you started. Then count: products in old store versus new store, orders in old store versus new store, customers, redirects, discounts, everything. If all counts match, you have moved what can be moved and you know what is missing. If a count does not match, find out why before you switch traffic over. Once the old store is deleted, you cannot go back. This step is what separates a successful move from a move that looks successful until customers and search engines find the broken pieces.
And then there is the part that actually loses businesses
If you do need a new store, the payments problem turns out to be the easy half. This is what is sitting in your current store right now, and what happens to each piece when someone tries to move it by hand:
Why this category in particular
A supplement store's data is dangerous to move by hand because compliance content lives in metafields. Batch numbers, testing certificates, ingredient sourcing notes and allergen flags are all reference or text metafields that a CSV export cannot carry — and if copied naively they keep pointing at files in the old store, so pages render but the compliance data is silently blank. On a regulated ingestible, that audit failure can trigger processor review even after onboarding.
| What you own | How much of it | What breaks doing it by hand | What we do instead |
|---|---|---|---|
| Product images | 1,250images≈ 5 hrsbulk re-upload, ~15 sec each | By handthe CSV carries image URLs and alt text, but they point at your OLD store's CDN — so the moment the old store goes, every image 404s. Re-upload and Shopify appends a dedupe suffix to the filename, which breaks every theme section and product description that referenced the original URL | Automatedevery file re-uploaded through the API with its alt text and variant attachment intact, its content type preserved so image-restricted fields still accept it, and every reference to the old URL rewritten |
| Product descriptions | 250descriptions≈ 2 hrsone pass to repair inline image links — the CSV carries the text | By handdescriptions are full of inline images and links pointing at the old store's CDN. Paste them into the new store and the text survives perfectly while every embedded image quietly dies — which you usually discover from a customer, not from a report | Automatedbodies copied verbatim, then a second pass rewrites every source-CDN URL inside them to the re-uploaded file on the new store |
| Product attributes & variants | 2,000variants≈ 45 minthe CSV carries these; the time is verifying option order | By handoption ORDER is part of the product's identity. Rebuild "Size, Colour" as "Colour, Size" and every theme swatch, saved customer URL and app that keys on variant position breaks — silently, because the product page still renders | Automatedvariants upserted by SKU with option names and order preserved, so swatches, deep links and app data keep working |
| Metafields & metaobjects | 3,000metafields≈ 20 hrsonly the reference, JSON and metaobject fields, ~1 min each | By handthe product CSV carries simple text and number metafields — but not metaobjects, and not reference or JSON types, which is exactly where app data and theme content live. Reference fields are the real trap: copy the value and it still points at objects in the OLD store, so the page renders and the custom block is silently empty | Automatedwritten in dependency order after their targets exist, with embedded references re-pointed at the new store's objects — and any value whose reference cannot be resolved is dropped rather than written broken |
| SEO data & redirects | 433records≈ 3 hrsredirects one at a time, plus a handle audit | By handany handle that changes becomes a dead URL with no redirect, and existing 301s are not in the product CSV at all. Years of accumulated ranking and backlinks end up pointing at pages that no longer resolve — the most expensive thing on this page to get wrong, and the slowest to notice | AutomatedSEO titles, meta descriptions and handles carried across, and every existing 301 recreated, so nothing that used to rank starts 404ing |
| Your custom theme | 1theme≈ 6 hrs2–10 hrs depending on how customised it is | By handa theme is not just its files. The settings, section content and block ordering are stored against the store, so a file copy gives you the layout and none of the content. Hardcoded asset URLs and tracking snippets also still point at the old store | Automatedyour live theme pulled and pushed as-is, then scanned for tracking snippets and hardcoded URLs that need re-pointing |
| Product videos | 15videos≈ 1 hrsre-upload and re-attach, ~4 min each | By handthe product CSV does not carry video or 3D media, so every one is a manual re-upload. They also cannot be pulled straight from a remote URL — the bytes have to be downloaded and staged first, and a wrong content type lands the file as a generic attachment that media-restricted fields then reject | Automatedvideo bytes downloaded, staged through a proper upload target, re-attached to the right product, and verified as processed rather than silently failed |
| Customers | 8,000customers≈ 2 hrsCSV import, then cleaning up the rows that fail | By handthe importer works, but marketing consent is the exposure: the CSV carries the current opt-in state and NOT the timestamp or source behind it. Re-opting someone in is a compliance breach, dropping them burns list revenue you paid for, and you cannot prove which happened afterwards. Default-address designation is also lost | Automatedcustomers upserted by email with every address, the default-address designation, and email and SMS consent states and timestamps preserved exactly as they were |
| Order history | 12,000orders≈ 8 hrsa paid third-party importer, plus a day of mapping and reconciliation | By handShopify's own CSV importer cannot create orders at all, so the hours here assume you buy a third-party importer — key them in by hand instead and 9,400 orders is closer to 390 hours, which is why nobody does that and why order history is simply abandoned in most DIY moves. Then support cannot answer a warranty claim, repeat-purchase segments are empty, and every returning-customer flow starts from zero. Getting the mapping wrong duplicates orders or re-dates them to today, and both are worse than not importing at all | Automatedfull order history recreated through the API with line items, properties, customers re-associated, original dates and tracking numbers intact |
| Navigation menus | 4menus≈ 1 hrsabout an hour to rebuild and relink them all by hand | By handmenu items store resource IDs, not paths, so nothing about them is portable — every link has to be re-pointed at the equivalent collection, page or product on the new store | Automatedmenus rebuilt with their nesting, and every item re-pointed at the equivalent object on the new store |
| Discount codes | 85discounts≈ 1 hrsabout 1 hr via the discount CSV, or ~3 hrs rebuilt by hand | By handthe discount CSV covers basic codes, but automatic discounts, quantity breaks and combination rules are not in it and have to be reconstructed by hand. A subtly wrong rule is worse than a missing one, because nobody notices until it has been over-discounting for a fortnight | Automateddiscounts recreated through the API with their rules, usage limits and dates intact, including automatic and free-shipping types |
| Gift card balances | 200gift cardsno manual routecannot be moved by anyone | By handthis is the one thing on this page that truly cannot be moved by anyone. Gift card codes are unreadable through EVERY Shopify API, by design — no tool, ours included, can copy them. Those balances are real money you owe real customers, and abandoning the old store does not abandon the liability: the customers still turn up expecting you to honour it | Automatedwe re-issue each card with an identical balance, customer and expiry date, and hand you the new codes as a CSV with customer email copy ready to send — the only honest way to move them |
| Blogs & pages | 63articles & pages≈ 4 hrsrecreated one at a time, ~4 min each | By handno CSV route for either. Articles also have no SEO fields of their own — their title and description tags live in metafields — so a hand-rebuilt blog loses its SEO even when every word of the text is right | Automatedarticles and pages recreated with authors, tags and publish dates, their SEO written to the metafields Shopify actually stores it in, and inline image URLs rewritten |
| Apps & app data | 10apps≈ 10 hrsabout 1 hr per app to reinstall, reconfigure and re-test | By handmost app data lives in metafields on your products and customers, so reinstalling the app gets you an empty app: reviews gone, subscription plans gone, loyalty balances gone, bundles gone. Flows and automations have to be rebuilt by hand and re-tested, and anything with its own billing has to be re-subscribed | Automatedthe metafield data your apps rely on migrates with the products and customers it hangs off, so a reinstalled app finds its data waiting instead of an empty store |
See these numbers for YOUR store, free
The figures above are a typical store in your category. The demo scan connects read-only to yours and counts the real thing — every product, variant, image, customer, order and metafield — then tells you exactly what a migration would carry across. No card, and it never writes to your store.
▶ Run the free demo scanDoes this need a new company?
A new legal entity does not reset your processing history. MATCH — the database processors use to screen high-risk merchants — follows the beneficial owner for five years, so opening a new company and applying again will flag the same decline reason. The only genuinely useful reason to form a new entity is to separate a compliant product line from a non-compliant one, but only if the entity structures are fully separate. Otherwise, save the cost and fix the claims.
Frequently asked
Will a new gateway turn my payments back on?
No. Your payments are off because a processor declined you, not because the gateway is wrong. A new gateway by itself does not fix the underlying reason — usually disease claims or a subscription refund dispute rate that is too high. You need an acquirer built for ingestibles, which means their underwriting focuses on your claims audit and your chargeback history, not a blanket refusal. The gateway you use is secondary. Find the acquirer first, then they will tell you which gateway to connect.
What reserve should I expect?
Most acquirers in this category hold 5–10% of your monthly volume in a rolling reserve, released 90–180 days after the transaction. The exact number depends on your volume, your chargeback rate and your supplier credentials. Larger orders and lower dispute rates get you to the lower end of that range. If you have a history of chargebacks or refunds from customers claiming the product did not work, expect the higher end or a longer hold period. Ask the acquirer upfront what they charge for this specific profile.
Do my product descriptions survive a store move?
Yes, if you migrate them correctly. The risk is that your claims descriptions — the exact language that triggers processor review — move with them word-for-word, and your new processor sees the same compliance problem the old one did. A migration is a good moment to audit every product page and rewrite disease claims as structure-and-function language. Do not just copy your old store. Use the move as a chance to fix the thing that got you declined in the first place.
What happens if I just rebrand and start over?
MATCH, the database processors use to screen merchants, follows the beneficial owner, not the company name. Opening a new store under a new business name with the same owner will flag the same decline reason. So you cannot evade an underwriting decision by rebranding. The only way forward is to fix the compliance problem — remove the claims, get the insurance and documentation — and apply to an acquirer who specializes in supplements with that profile fixed. It is slower, but it is the honest path.
Can I just export and import the CSV and call it done?
Not unless your store contains only text fields and product SKUs. Shopify's CSV export leaves behind metafields, metaobjects, orders, gift card codes, videos, themes, menus, discounts and redirects. The things most stores rely on. You can move the CSV, but then you have half a store. You need a plan for each missing category before you go live.
What happens to my customer data and order history?
Orders do not export through CSV. You must download them separately from your reports or ask Shopify support for an export. Customer email addresses and account records do not appear in CSV either — those must be exported separately as well. Customer data is critical, especially if you have consent timestamps for email marketing. Treat orders and customers as a separate export, verify the counts match the old store, and keep that list safe before you delete the old store.
Will my gift card codes transfer?
No. Gift card codes cannot be read through any Shopify API — no one can extract them, not even Shopify. That means they cannot be automatically moved. You must issue new gift cards in the new store. If you have outstanding balance on old codes that you want to honor, you will need to track and re-issue manually, or accept the loss. Check what gift cards you have issued before the move so you know what you are dealing with.
What about my theme and navigation menus?
Themes and menus do not export through CSV. You must select a theme in the new store and configure it from scratch, or pay a developer to replicate your current theme's customizations. Navigation menus must be rebuilt manually. If you used a third-party app to manage menus, check whether that app can export and re-import. The theme and navigation are visible to every customer, so do not skip them.
How do I know nothing was left behind?
Count everything. Before you go live, export the old store's data one more time. Import it into the new store again. Then compare: product count, order count, customer count, discount count, redirect count. If counts match, you have moved what can be moved. If a count is off, investigate why before you switch traffic. Do not assume the migration is complete until you have verified it. Once the old store is deleted, verification becomes impossible.
Move everything, verified twice, from $247
Pick a package and the migration order form unlocks immediately. Your existing store is only ever read from — we never write to it, so nothing you still have can be made worse. How the migration runs, step by step →