How to handle ecommerce when you migrate from QuickBooks to Business Central

Short answer.

The answers usually point clearly at Abakion B2B Ecommerce, at Shopify, or at keeping the storefront you have, and knowing which one you're facing is worth more than assuming the migration tool covers more than it does.

QuickBooks is the only system in this series that Microsoft built a migration tool for, and there are two: a QuickBooks Desktop Data Migration extension and a QuickBooks Online Data Migration extension, both installed as part of Business Central's Data Migration assisted setup. Both move customers, vendors, items, chart of accounts, beginning balances, on-hand quantities and open invoices, and both state in their own documentation that they do not migrate purchase orders or sales orders. So the accounting migrates and the storefront doesn't, and there's no second route that rescues order history, because Business Central's Shopify Connector can't import archived Shopify orders either.

Two routes make Business Central the system of record: move B2C to Shopify with Microsoft's Shopify Connector, or move B2B into Business Central with Abakion B2B Ecommerce. Keeping the storefront and the inventory mid-tier and rebuilding only the accounting link is the third route, and for many QuickBooks companies it is the smallest change.

What are the three options, and how do they compare?

There are three real options for ecommerce when you migrate from QuickBooks to Business Central, and for a QuickBooks company the first is often the smallest change.

1. Keep the storefront and the mid-tier, and rebuild only the accounting connection. Check your vendor's Business Central support first, because several of the biggest names in QuickBooks ecommerce don't have any.
2. Move B2C to Shopify and use Microsoft's Shopify Connector.
3. Move B2B into Business Central with the Abakion B2B Ecommerce app.

The other two make Business Central the system of record, and they split by who you sell to.

Is there a migration tool from QuickBooks to Business Central?

Yes, two of them, and they're already installed. The QuickBooks Desktop Data Migration extension and the QuickBooks Online Data Migration extension are part of Business Central's Data Migration assisted setup, and Microsoft's own advice is to use the wizards rather than configuration packages.

So this should be the easy one. And on the accounting side, it more or less is.

Then you read the documentation. Both extension pages carry the same note, in the same place, in the same words: we do not migrate purchase orders or sales orders.

Your accounts migrate with a wizard. Your orders don't migrate at all.

That single sentence draws the line this whole article is about, because look at what the wizard does move:

• customers and vendors
• items
• chart of accounts
• general ledger beginning balance transactions
• on-hand quantities for inventory items
• open customer and vendor documents such as invoices, credit memos and payments

That's the accounting, precisely and completely.

And look at what it leaves. Orders, order history, product content, pricing rules, variants, and partial payments, because Microsoft states that only full amounts on sales and purchase documents are migrated, so a customer who has paid 300 of a 500-dollar invoice arrives owing 500. Transactions also land unposted, and Microsoft notes that beginning balances may need correcting because QuickBooks doesn't store the current balance for all accounts.

One premise before we go further. Business Central here means Business Central online. Microsoft states that you can't install Marketplace apps on-premises, including in Docker-based deployments, so on-premises isn't a realistic destination for anybody who needs connector apps, and we won't cover it.

Is QuickBooks Desktop being discontinued?

Not for existing subscribers, but Intuit stopped selling it to new ones. As of 1 October 2024, Intuit no longer sells new US subscriptions of QuickBooks Desktop Pro Plus, Premier Plus, Mac Plus or Enhanced Payroll.

Existing subscribers can keep renewing, and Intuit says it will continue to provide security updates, product updates and support for them. QuickBooks Desktop Enterprise is still sold, in Silver, Gold, Platinum and Diamond. But there are no Pro or Premier product pages left on Intuit's US site, and the headline on Intuit's own Desktop page now reads "Level up from QuickBooks Desktop", offering three destinations: QuickBooks Desktop Enterprise, QuickBooks Online Advanced, and Intuit Enterprise Suite.

What are the limits that make companies leave QuickBooks?

Intuit publishes them, which makes them useful.

QuickBooks Desktop Pro and Premier are limited to a 14,999 list limit and, in Intuit's words, small data files. Enterprise raises that to a million names and a million items, and Intuit describes Enterprise as six times the capacity of Pro and Premier. On users, Intuit's comparison says Pro and Premier limit you to five users, while Enterprise goes up to 40 on Diamond.

QuickBooks Online limits are different in kind. Inventory tracking is available in Plus and Advanced only, so Simple Start and Essentials have none. Plus gives five billable users and 40 classes and locations, Advanced gives 25 users and unlimited classes and locations. And QuickBooks Online locations are a reporting dimension rather than stock-holding sites.

Two more, and these are the ones that catch B2B sellers. Advanced Pricing, which is where price rules by customer, class, item category or quantity actually live, is included in the Platinum and Diamond Enterprise subscriptions only. Advanced Inventory, which is what gives you multiple inventory sites, bin location tracking and serial or lot numbers, is also Platinum and Diamond only.

So a QuickBooks business selling online at any scale is either paying for the top two Enterprise tiers, or doing its inventory and its pricing somewhere else entirely.

Is my inventory actually in QuickBooks?

Probably not, and this is the part that decides how big your project is. You can check it in five minutes.

Look at what sits between your store and your accounts. In the QuickBooks world it's usually Webgility, Fishbowl, Katana, Cin7, SOS Inventory or Linnworks, and every one of those describes itself the same way. Fishbowl says it runs alongside your existing QuickBooks account, syncing inventory, purchasing, manufacturing and warehouse operations to your QuickBooks general ledger. Katana keeps the sales orders and creates invoices in QuickBooks from them. SOS Inventory calls itself inventory, order management and manufacturing for QuickBooks Online.

The pattern is clear. The mid-tier holds the stock and the orders, and QuickBooks receives the journal.

Which matters for a reason that has nothing to do with QuickBooks. Most of those vendors don't go to Business Central at all. Webgility lists QuickBooks Online, QuickBooks Desktop and Xero. Fishbowl supports all three QuickBooks flavors and no Business Central, and its own comparison table notes that Cin7 and Katana are QuickBooks Online only. Linnworks lists QuickBooks Online under accounting and nothing else. The connectors that do reach Business Central are the general-purpose integration platforms, Celigo, Workato, DBSync and Codat, which is a different product at a different price.

So for a lot of readers this migration replaces two systems rather than one, and that's worth knowing before anybody quotes it as an accounting project.

Does the QuickBooks Online API work like the Business Central API?

Yes, structurally, and that makes a QuickBooks Online storefront integration a rewrite rather than a rethink.

QuickBooks Online has a REST API with OAuth 2.0, and connectors use it to push orders, refunds, products, inventory and payout fees. Quantity lives on the item rather than in a separate stock endpoint, and there are per-company rate limits worth checking against your traffic. Business Central online is the same shape: HTTPS, tokens, entities, and in Microsoft's words the only supported option for reading data is using APIs. The people who built your QuickBooks Online integration will recognize what they're building.

How does QuickBooks Desktop connect to a web store?

Through the QuickBooks Web Connector, which polls. Intuit's own programmer's guide calls it an upside-down communication model, where the Web Connector initiates the session with the web service over HTTPS and asks the web service whether it has work for QuickBooks.

The store never talks to QuickBooks. It waits to be asked. And the schedule can't be set below one minute through the interface.

There's a detail in that document that says more than any analysis could. The current file at Intuit's SDK path identifies itself as Web Connector version 2.0, released May 2009.

Your QuickBooks Desktop integration doesn't call your accounts. It waits for a Windows utility to phone out and ask whether it has anything to say.

Business Central online has no equivalent and needs none. Nothing polls, nothing has to be running on a particular PC, and nothing stops working because somebody closed the company file.

There's an awkward pairing worth pointing out in the Desktop migration path, and it's a scheduling fact rather than a criticism. Microsoft's Data Exporter Tool for QuickBooks Desktop is documented as working with QuickBooks 2017 and 2018, on a page whose own metadata dates it to 2021, and Intuit stopped selling Pro and Premier to new US subscribers in October 2024. If you're on a newer Desktop release, confirm what the exporter will actually read before you plan around it, and expect to do at least some of the load through configuration packages.

Do item numbers and customer records change when I move from QuickBooks to Business Central?

Yes, and the reason is structural rather than a question of field length.

Business Central's item `No.` is a `Code[20]`, and the `Code` data type converts to uppercase and strips leading and trailing spaces. Microsoft's own example is that a code of `' 2 '` becomes `'2'`, one character long. So a Business Central item number is twenty uppercase trimmed characters, and it's an identifier rather than a label.

QuickBooks organizes items in a parent and sub-item hierarchy, so the identity of an item is its position in that hierarchy rather than a flat code. If your storefront has been matching on QuickBooks item names, check what those names actually look like in the export before you assume they map to anything. A name built from a category path isn't an item code, and turning one into the other is a decision rather than a conversion.

What does QuickBooks not have that Business Central does?

Three things, and they're the reason this migration is an opportunity rather than a salvage job.

No product variants. Your Shopify store has them, so today either Shopify holds the variant model on its own and QuickBooks sees separate items, or your mid-tier reconciles the two. Business Central models a range as one item with a `Code[20]` number plus Item Variant records with a `Code[10]` code, so somebody has to decide which of your QuickBooks items were ever really separate products.

No product content layer. No item images, no attributes, no options, no marketing descriptions. Your web copy and photography live in Shopify, and nothing in the migration path touches them, because there's nothing in QuickBooks to move. Business Central has item attributes, of option and variable types, assignable to items and to item categories with inheritance, filterable, and Microsoft's documentation names integrated web shop searches as a reason they exist.

No standard multi-location inventory. Multiple stock sites are a Platinum and Diamond Enterprise feature in QuickBooks Desktop and absent in QuickBooks Online. In Business Central, locations are standard, with transfer orders and transfer routes, and Microsoft notes that many fields on the location card aren't relevant for companies without complex warehouse needs. So you get more than you had, and you also inherit a design decision, because your store's availability logic gets rebuilt on top of whatever locations you choose.

How does QuickBooks pricing map to Business Central pricing?

The functionality you pay extra for in QuickBooks is standard in Business Central, and it's expressed differently.

Business Central price lists apply to a customer, a customer price group or a campaign, keyed on the item or item discount group, with unit of measure, minimum quantity, start and end dates and currency on the line. The rule is that the best price is the lowest price with the highest line discount allowed on a given date, resolved in two passes: first whether an agreement exists for this customer or their group and this item or item discount group inside the date window, then whether the minimum quantity and currency requirements are met.

All of that is standard in every Business Central tier. In QuickBooks the equivalent is Advanced Pricing, which is Platinum and Diamond Enterprise only, and which Intuit describes as customizable and automated price rules by sales rep, class, customer or job type, item category or vendor, with volume discounts set as a fixed percent off a set quantity.

So one of two things is true today. Either you're paying for the top Enterprise tiers and your price rules need re-expressing as price list lines with minimum quantities and date ranges. Or your customer pricing isn't in QuickBooks at all, in which case it's in the store or the mid-tier, and this migration is the first chance you've had to put it in the same system that knows the cost and the stock.

And if Shopify is on your shortlist, there's a hard limit to know now rather than later. Microsoft documents that the connector calculates a price by creating a temporary sales quote for the item at a quantity of one and using standard price calculation, so only prices and discounts applicable at quantity one are used, and you can't export different prices or discounts based on quantity. If your customers get volume discounts, that sentence decides the architecture on its own.

What happens to order history?

Nothing happens to it automatically, and there's no second route that rescues it either. This is the decision to make first, not last.

Neither migration extension moves sales orders. And Business Central's Shopify Connector imports orders that aren't archived and were created or modified since the last sync, with Microsoft stating plainly that you can't import orders that are archived in Shopify. The documented workaround is to unarchive them in the Shopify admin first, and Microsoft suggests turning off Shopify's automatic archiving. So there's no historical order import feature on that side either.

Put those two facts together and you have three legitimate options, all of which need choosing deliberately:

• history stays queryable in the old system, as a read-only QuickBooks file or a QuickBooks Online archive
• history is loaded as opening balances only
• history is rebuilt from the storefront's own records

Discovering the question the week before go-live is what you're avoiding.

Will my customers' web store logins still work?

Yes. They never existed in QuickBooks, so they live in your storefront and survive untouched.

What breaks is the key. If item names or customer records get renumbered on the way into Business Central, saved carts, reorder lists and account pages stop resolving even though every record survived.

What about US sales tax?

It ports cleanly, which is the single least complicated part of this migration.

Avalara publishes an AvaTax connector for Business Central as well as for QuickBooks Online, QuickBooks Desktop and Intuit Enterprise Suite, so the tax engine is the same vendor at both ends.

If Shopify is in the picture, you'll have two. Shopify helps automate charging sales tax at checkout and states that it doesn't remit or file your taxes unless you use Shopify Tax with automated filing, while Avalara sits behind Business Central for posting and returns. Two engines, and they need to agree.

When does the Microsoft Shopify Connector fit?

When you sell to consumers, or to business customers whose pricing works at a single quantity tier, and you're selling through one storefront rather than several marketplaces.

Architecture. The Shopify Connector is built by Microsoft, ships preinstalled with Business Central online, and runs on the job queue. There's no middleware to license, no server, and nobody in the middle.

Data flow. Item sync is bidirectional and covers variants, images, barcodes, vendor item numbers, tags and metafields, and it exports item attributes, extended and marketing texts and translations. Inventory syncs across the locations you select. Customers and companies sync both ways, with mapping on email, phone or registration number.

Orders. Order import covers the Shopify online store, Shopify POS and Shopify B2B, and brings shipping costs, gift cards, tips, refunds, cancellations and payouts from Shopify Payments. Fulfillment tracking goes back to Shopify, and posted sales invoices are exported.

Tax. Shopify calculates sales tax at checkout, and Avalara sits behind Business Central for posting and filing.

Limits. Prices export at quantity one only, so volume breaks don't travel. A Shopify variant matrix combining two or more options can't be created by the connector, because Business Central has no option matrix, and setting SKU mapping to vendor item number or barcode prevents variant creation entirely. Archived Shopify orders can't be imported. Extension points are deliberately few, so Microsoft can follow Shopify's release pace without breaking changes. It's one shop per configuration, so Amazon and Walmart and eBay need something else. And you have to stay current on Business Central versions.

That last point is the one for QuickBooks sellers specifically, because marketplace selling is common in this base and it's exactly what one shop per configuration doesn't cover.

When does Abakion B2B Ecommerce fit?

When you sell to trade customers on their own prices and they reorder, which describes most QuickBooks distributors and manufacturers.

Architecture. Abakion B2B Ecommerce installs as an app in Business Central, the site runs on Azure, and the storefront reads live data from Business Central. There's no synchronization job, no staging database, no integration to own, and nothing to regression test twice a year.

Data flow. Customer-specific catalogs, prices, agreements and currencies come straight from the ERP, and delivery dates come from Business Central's own availability calculation. Order history and reorder work from actual posted documents.

Product content. The accompanying Master Data Information app handles product content and variant matrices, and for a QuickBooks company that's genuinely new capability rather than a migration, because your product content has never had anywhere to live except the storefront.

Tax. Avalara is supported for US sales tax, which is very likely the engine you already use.

Commercial shape. Fixed price on the initial project, then a subscription tiered by the number of active customers and the number of items in the store.

The argument that lands hardest for a QuickBooks customer. Today the price might be in the store, the stock is in the mid-tier, the invoice is in QuickBooks, and somebody reconciles. With a storefront reading Business Central directly, there's nothing to push out to the store, because there's no out.

In what order should you sequence the two projects?

The accounts first, the storefront once afterward, and the order history decision before either.

The most expensive mistake available to you is spending money on the QuickBooks integration in the year before you replace QuickBooks. Every hour spent on a Web Connector job or a mid-tier mapping is written off on go-live day, so design any change to the current setup as thin and disposable and let the storefront land once, on the model you intend to keep. Two web projects in two years is the outcome nobody plans for and plenty of companies get.

There's a QuickBooks specific trap. Moving from QuickBooks Desktop to QuickBooks Online first, as an interim step, looks reasonable and changes your integration completely, because the Web Connector goes away and the REST API arrives. If you're going to Business Central eventually, that's a rewrite you'll do twice.

And do the order history decision in the same conversation where you set the go-live date, because it's the only thing here with no supported tooling on either side.

When is neither Shopify nor Abakion B2B Ecommerce enough?

When your store has to do something both routes deliberately trade away. Neither option fits if you:

• sell configurable products
• run punchout or EDI into your customers' procurement systems
• sell across several marketplaces
• operate a subscription model
• run a design-led consumer brand where the storefront is the marketing
• need volume discount pricing published to a Shopify catalog

Marketplaces are the one that catches QuickBooks sellers most often, because Amazon and Walmart and eBay alongside your own store is normal in this base, and it needs a mid-tier. If that's you, the realistic outcome is that the mid-tier stays and Business Central becomes the financial and inventory backbone underneath it, which is a smaller change than the other two routes and a perfectly respectable place to land.

But plenty of companies assume they're in that group without testing it, keep three systems in sync by hand, and never find out that most of what the mid-tier was doing was compensating for a 14,999 item limit.

Where to start

Five questions, and you can answer all of them this week.

1. What actually holds your inventory and your orders: the store, a mid-tier, or QuickBooks?
2. Are you on QuickBooks Desktop or QuickBooks Online, and if Desktop, which edition and tier? Advanced Pricing and Advanced Inventory are Platinum and Diamond only, and their absence tells you where your pricing and stock really live.
3. Does your mid-tier or connector vendor support Business Central at all?
4. What do your QuickBooks item names look like, and does your store match on them?
5. What do you want to happen to order history, and who owns that decision?

The answers usually point clearly at Abakion B2B Ecommerce, at Shopify, or at keeping the storefront you have, and knowing which one you're facing is worth more than assuming the migration tool covers more than it does.

Frequently asked questions

Both apps are on Microsoft Marketplace

• Shopify Connector, published by Microsoft
• Abakion B2B Ecommerce
• Abakion B2B Ecommerce product page

Sources

• QuickBooks Data Migration extension, Microsoft Learn
• QuickBooks Online Data Migration extension, Microsoft Learn
• Changing from a QuickBooks app to Business Central, Microsoft Learn
• Migrate on-premises data to Business Central online, Microsoft Learn
• Import business data from other finance systems, Microsoft Learn
• Migrate to the cloud from any SQL database, 2026 release wave 1, Microsoft Learn
• Synchronize items with Shopify, Microsoft Learn
• Synchronize orders with Shopify, Microsoft Learn
• Shopify Connector overview, Microsoft Learn
• Item table reference, Business Central, Microsoft Learn
• Item Variant table reference, Business Central, Microsoft Learn
• Location table reference, Business Central, Microsoft Learn
• Code data type, Business Central, Microsoft Learn
• Set up locations, Business Central, Microsoft Learn
• Work with item attributes, Microsoft Learn
• Record sales price, discount and payment agreements, Microsoft Learn
• Design details, costing methods, Microsoft Learn
• Installing and uninstalling extensions in Business Central, Microsoft Learn
• QuickBooks Desktop support directory, Intuit
• Level up from QuickBooks Desktop, Intuit
• QuickBooks Desktop Enterprise, Intuit
• Compare Pro and Premier to Enterprise, Intuit
• QuickBooks Desktop Enterprise multiple users, Intuit
• QuickBooks Desktop Enterprise Advanced Inventory, Intuit
• QuickBooks Desktop Enterprise Advanced Pricing, Intuit
• QuickBooks pricing and plans, Intuit
• QuickBooks inventory management, Intuit
• QuickBooks Web Connector Programmer's Guide, Intuit
• Avalara integrations for Microsoft Dynamics, Avalara
• Avalara integration for QuickBooks, Avalara
• US taxes, Shopify Help Center
• Shopify Tax, Shopify Help Center
• Webgility integrations, Webgility
• Fishbowl QuickBooks inventory management, Fishbowl
• Katana integrations, Katana
• Cin7 integrations, Cin7
• SOS Inventory, SOS Inventory
• Linnworks integrations, Linnworks
• Codat accounting integrations, Codat