What doesn't convert to QuickBooks Online

The list, grouped by how much it matters

Intuit publishes what does not carry across. It is accurate and it is long. What it does not do is separate the items that cost you an afternoon from the items that change your reported profit, so everything reads at the same weight and the three that matter get lost in a list of forty.

Here is the same material sorted by consequence.

Changes your numbers. Inventory valuation. Sales tax payments. Payroll detail for prior years.

Costs you rework. Budgets, memorized reports, memorized transaction groups, custom templates, price levels, progress invoicing links, open purchase order connections, units of measure.

Gone, and you will not get it back. Audit trail. Past reconciliation reports. Mileage records.

Quietly reshaped. Estimates, assemblies, item hierarchies deeper than five levels, multiple A/R and A/P accounts, multi ship-to addresses.

Group	Items	What it costs you
Changes your numbers	Inventory valuation, sales tax payments, prior-year payroll detail	Reported profit and filings, until corrected
Costs you rework	Budgets, memorized reports and transaction groups, custom templates, price levels, progress invoicing links, purchase order links, units of measure	An afternoon of rebuilding
Gone for good	Audit trail, past reconciliation reports, mileage records	Keep the Desktop file to answer questions about them
Quietly reshaped	Estimates, assemblies, item levels past five, extra A/R and A/P accounts, extra ship-to addresses	Reports and lists that read differently than before

The rest of this post is the first group, because those are the ones that produce a file nobody can tie out, and then a cleanup.

Inventory is rebuilt on FIFO, and your COGS moves

This is the single most consequential thing on the list, and it is the one most migration guides mention in a half sentence if at all.

QuickBooks Desktop Pro, Premier and Mac value inventory at average cost. QuickBooks Online values it at FIFO. There is no setting that reconciles the two. When the file converts, you set a FIFO start date and QuickBooks Online recalculates inventory from that date forward, posting whatever adjustments the new method requires.

So the cost of goods sold on your migrated profit and loss is not the cost of goods sold on the Desktop file you migrated from. Not because anything went wrong, but because you changed valuation methods in the middle of a fiscal year and the software did what you asked. On a business holding a few thousand dollars of stock the gap is noise. On a distributor or a contractor carrying real inventory across thousands of line items, it is large enough that the first post-migration P&L reads as though the business had a different year.

Intuit’s own community has a thread titled “Cost of Good Sold account is way off after migration with inventory.” It is not a bug report. It is the method change, arriving as a surprise.

If the file carries meaningful inventory, decide the valuation question before the migration rather than discovering it afterwards, and tell whoever prepares the return that the basis changed and on what date.

Sales tax payments land on the wrong filings

Sales tax transactions convert. The payments against them do not land where they belong.

Intuit’s guidance is blunt about the fix: delete the migrated sales tax payments, then recreate them in the QuickBooks Online sales tax centre. That is the documented remedy, not a workaround somebody invented.

What makes this expensive is that it looks fine. The liability account has a balance, payments exist, and nothing on the balance sheet is obviously wrong. The error is in which filing period each payment is applied to, which surfaces the next time somebody files a return and the numbers do not match what the system expects. If the business files monthly, that is a problem four weeks after the migration, long after anyone is still watching for migration issues.

Check this in the first week, not the first quarter.

Payroll arrives as year-to-date lump sums

QuickBooks Online copies the current year’s paycheck information as lump sums rather than individual paychecks. Prior year payroll detail does not come across at all, only the balances.

For most files that is survivable, because the returns for prior years are already filed and the detail lives with the payroll provider. It stops being survivable in two cases. The first is an amended return, where you need the individual runs and they are now only in a Desktop file somebody may have stopped paying for. The second is a business partway through its first year on a new payroll system, where the year-to-date figures are the only record of how the totals were built.

Two smaller payroll items that catch people out: employees in Puerto Rico, American Samoa and the US Virgin Islands arrive with blank addresses, and inactive employees who were paid in the current tax year come back as active.

Check the file size before you plan anything

This is the first step of converting a Desktop file, and the one that decides which QuickBooks Online plan you can promise.

Press F2 or Ctrl+1 in QuickBooks Desktop and read the total targets from the Product Information window. Targets are line-level records, not transaction counts, so the number is larger than most people expect.

Three thresholds decide what happens next.

• Under 350,000. Any QuickBooks Online plan will take the file.
• 350,000 to 750,000. Only QuickBooks Online Advanced will accept it, which is a materially different subscription price and worth knowing before you promise a client a plan.
• Over 750,000. The migration still runs up to the hard ceiling, but expect discrepancies, inventory first among them, and expect it to take a long time.
• Over 4,000,000. Refused. The file has to be condensed first, and condensing is itself a decision about how much history you are willing to lose.

The other clock worth knowing: you have 90 calendar days to complete the transfer if the QuickBooks Online company was created by self-signup, and 180 if an accountant created it. That is a reason to have an accountant start the company even when the client could do it themselves.

Some things do convert, against expectation

Worth knowing so you do not rebuild them.

Reconciled transactions keep their cleared status, marked R, even though the reconciliation reports themselves are gone. The closing date password transfers. Bank feed rules transfer in Express and Advanced modes. Logos transfer even though the templates built around them do not.

So a migrated file is not unreconciled. It is reconciled with no evidence, which is a different problem and a smaller one.

Prove what happened, rather than assuming

The migration tool reports success or failure. It does not report accuracy, and the difference between those two is where the work is.

Before you close the Desktop file, run a trial balance as of the migration date and keep it. Run the same report in QuickBooks Online once the import finishes and compare them line by line. Where they differ, the difference is either inventory valuation, sales tax, or payroll, and you now know which of the three to open first.

Do this while you still have the Desktop file open and licensed. A trial balance you cannot reproduce is not a control. The six checks to run after a migration start from that comparison and work outwards.

If the comparison shows the file has drifted further than the three known causes explain, that is a cleanup rather than a migration problem, and it is priced by how many months are affected:

$99per month of backlog20% off 6+ months

The one-line version

Nothing about the migration is dishonest, and most of what does not convert is an inconvenience. Three items are not: inventory changes valuation method, sales tax payments apply to the wrong periods, and payroll loses its detail. Everything else on Intuit’s list can be rebuilt on a slow afternoon.

If the file is already wrong before it moves, migrating it produces a wrong file in a new place. Cleanup comes first in that case, and whether to repair or start fresh is the diagnostic for files that have drifted too far to be worth carrying across. Whether a file has to move yet depends on its Desktop version, and the current end-of-life dates settle that. The migration page has what we do and what it costs, and a free file review says which group a given file falls into before anything moves.