Most of your lists and transactions come over. What doesn't transfer cleanly, per Intuit's own migration documentation, includes: sales orders (they don't exist in QuickBooks Online), most payroll history, your inventory valuation method, attachments, custom templates and form designs, bank feed rules, memorized reports, and parts of your sales-tax history.
And one that surprises everyone: you can't selectively re-migrate later. A second upload replaces everything you've already moved.
The pitch for moving to QuickBooks Online is that "everything comes over." Most of it does — your chart of accounts, customers, vendors, and the bulk of your transaction history land on the other side. But the gaps are specific, they're documented by Intuit itself, and for a construction material supplier several of them hit the exact parts of the business that keep the lights on. Here's the honest list, and what to do about it before you commit.
01Sales orders — gone entirely
QuickBooks Online has no sales order transaction type, so sales orders do not migrate. This is the big one for suppliers. The sales order is the non-posting commitment that reserves stock, drives fulfillment, and tracks backorders — and it simply has no home in QuickBooks Online. There's nothing to convert it to. If your operation runs on sales orders, this isn't a data-loss footnote; it's your workflow disappearing. In QuickBooks Desktop a sales order reserves stock and splits into backorders; in QuickBooks Online that reserved quantity isn't tracked, which is how suppliers oversell and chase phantom demand. Here's the full breakdown of the sales order gap and how to get it back. Or run the free audit →
02Most of your payroll history
Only the current year's paychecks come over, and they convert as lump-sum regular checks — not detailed payroll transactions. Per Intuit's documentation, prior-year employee year-to-date figures, payroll item breakdowns, and the granular detail behind each check don't carry over. Liability refunds and adjustments are converted into journal entries, and some employee addresses can come across blank. Suppliers running assisted payroll on QuickBooks Desktop often find there's no clean equivalent on the other side, and end up paying for both products during the overlap while they sort it out.
03Your inventory valuation method
QuickBooks Online only does FIFO, so if you ran average cost in QuickBooks Desktop, your inventory is recalculated. During migration you're asked to set a FIFO start date, and QuickBooks Online recomputes inventory from there. For a supplier carrying thousands of SKUs, that can shift valuations and cost of goods sold versus what your old reports showed. Inventory tracking is also only available on the Plus and Advanced plans — not Simple Start or Essentials.
04Sales-tax payment history
There's a documented sales-tax limitation: payments you made in QuickBooks Desktop can apply to the wrong filing periods in QuickBooks Online. Intuit's own guidance is to delete the migrated sales-tax payments and recreate them in the QuickBooks Online sales tax center. Some taxes also move as journal entries, and sales tax won't copy for every transaction. If you're not watching for it, your filings can look wrong out of the gate.
05Attachments and documents
Attachments aren't part of the main migration. They move through a separate process and only when they're 30MB or smaller and stored on your computer's hard drive. In practice, a lot of suppliers find that the POs, signed deliveries, and vendor documents they'd attached to transactions need to be re-attached by hand after the move.
06Custom templates, form designs, and custom fields
Your custom invoice, estimate, and purchase order templates don't transfer — you rebuild them in QuickBooks Online. The form designer, custom fields, and branded layouts you fine-tuned over years in QuickBooks Desktop don't carry across, and QuickBooks Online's customization options are more limited. Budget time to recreate anything a builder expects to see on your paperwork.
07Memorized items, bank rules, and reports
Memorized transactions convert to recurring transactions, but memorized transaction groups don't migrate, and start dates drop off. Bank feed rules behave differently in QuickBooks Online and generally need to be rebuilt. Memorized and custom reports don't come over either — so the saved reports your team runs every week have to be recreated from scratch.
08The structural remaps nobody mentions
Some things technically "transfer" but change shape in ways that trip people up:
- Jobs become projects or sub-customers. Leaf-level jobs migrate as projects; the rest become sub-customers — a different structure than the job hierarchy you knew.
- Only one default A/R and one default A/P account are allowed in QuickBooks Online, even if QuickBooks Desktop used more.
- Customers with no balance import as inactive (effectively deleted), so your active customer list can look thinner than expected.
- Budgets are limited — Profit and Loss budget types convert, but not everything you may have set up.
The one that really stings: you can't selectively re-migrate. If payroll or inventory comes over wrong and you try a fresh upload to fix just that piece, the new upload completely replaces everything already in your QuickBooks Online company — including the corrections you've made by hand since. Get it right the first time, or be ready to redo work.
Why this hits a supplier harder
Read that list again through a supplier's eyes. The sales order — your commitment and fulfillment record — is gone. Multi-vendor purchase order consolidation was never native to QuickBooks Online to begin with. Builder and lot tracking has nowhere structured to live. So you're not just losing some history in the move; you're losing the operational layer that made QuickBooks Desktop usable for running a supply business, on top of the data gaps every business hits.
That's the gap ClearOrder was built to fill: it restores a true sales order workflow, multi-vendor PO consolidation, and builder and lot tracking on top of QuickBooks Online, so the move to the cloud doesn't cost you the way you actually operate. Your books still live in QuickBooks Online; your operation lives in ClearOrder.
See what's at risk in your own file
Before you commit to the migration, run ClearOrder's free pre-migration audit on your QuickBooks Desktop export. It flags what's at risk — record counts, duplicates, ghost orders — in under a minute, entirely in your browser. Nothing is uploaded.
Run the Free Audit → Book a Demo