What to check after a QuickBooks migration

The checks, in order

The migration tool tells you whether the import completed. It does not tell you whether the result is right, and those are different questions. A file can import cleanly and still carry a balance sheet nobody can tie to the one you had last week.

Six checks. Run them in this order, because the first one tells you which of the other five to bother with. To record both files’ figures side by side: download the check sheet (Excel).

1. Trial balance, both files, same date. The control everything else hangs off.
2. Inventory valuation summary. Where the largest differences live.
3. Sales tax payments and the periods they apply to. The one with a deadline attached.
4. Payroll year to date against the provider’s own reports.
5. Open purchase orders and estimates. Status and linkage, not amounts.
6. A/R and A/P aging, tied back to the balance sheet.

Check	Compare against	A difference usually means
Trial balance	The Desktop trial balance, same date	Read which accounts differ; the pattern names the cause
Inventory valuation summary	The Desktop report, same date	Expected: average cost became FIFO. Record the variance
Sales tax payments	The periods each payment should settle	Payments applied to the wrong filings
Payroll year to date	The payroll provider’s own summary	Current-year paychecks arrived as lump sums
Open purchase orders and estimates	Their status and links	Orders unlinked from bills; active estimates now closed
A/R and A/P aging	The balance sheet totals	Desktop used more than one A/R or A/P account

Do this in the first week. Every one of these is cheaper to fix while the Desktop file is still open and licensed, and most of them are invisible until something downstream breaks. If the migration has not happened yet, how to convert QuickBooks Desktop to Online covers the preparation, including saving the trial balance this list starts from.

Check 1: Trial balance on both sides

Run a trial balance in QuickBooks Desktop as of the migration date. Run the same report in QuickBooks Online. Put them side by side.

If they agree, the rest of this list is a formality and you should still run it, because two of the checks below can pass a trial balance and still be wrong.

If they disagree, note which accounts differ before you investigate any of them. The pattern tells you the cause faster than the amounts do. Differences concentrated in inventory and cost of goods sold are the valuation method. Differences in a sales tax liability account are the payment application. Differences in wage and tax accounts are the payroll lump sums. Differences spread evenly across dozens of unrelated accounts are not a migration problem at all, they are a file that was already wrong.

Save both reports as PDFs. A comparison you cannot reproduce in six months is not evidence, and the question does come back at year end.

Check 2: Inventory valuation summary

Desktop Pro, Premier and Mac value inventory at average cost. QuickBooks Online uses FIFO and recalculates from a start date you set. So this report is expected to differ, and the job is to establish by how much and to write it down, not to make it match.

Run the inventory valuation summary in both files as of the same date. Record the total asset value and the variance. That number belongs in an email to whoever prepares the return, because the basis of the business’s inventory changed on a specific date and that is a tax preparer’s decision to handle, not a bookkeeper’s to absorb quietly.

What doesn’t convert covers why the method change happens and when it is worth deciding before the migration rather than after.

Check 3: Sales tax payments

This check exists because Intuit’s own guidance says the payments apply to the wrong filings, and the documented fix is to delete the migrated payments and recreate them in the QuickBooks Online sales tax centre.

Open the sales tax centre. For each period that should be settled, confirm the payment is applied to that period rather than sitting against another one or unapplied. The liability balance can be correct in total while every payment inside it is attached to the wrong month, which is why reading the balance is not enough.

Put this ahead of the checks below it for one reason: a wrong filing period has a due date behind it. Everything else on this list waits.

Check 4: Payroll year to date

The current year arrives as lump sums rather than individual paychecks, and prior years arrive as balances with no detail underneath them.

Pull the year-to-date summary from the payroll provider, not from QuickBooks, and compare gross wages, each tax, and employer contributions line by line. The provider is the source of record here and QuickBooks is the copy.

Two specific things to look at while you are in there. Employees in Puerto Rico, American Samoa and the US Virgin Islands arrive with blank addresses. Inactive employees who were paid at any point in the current tax year come back marked active, which means they will appear in lists and reports that should not include them.

Check 5: Open purchase orders and estimates

Neither of these moves money, which is why they get skipped, and why they surface weeks later as a confused conversation with a customer.

Open purchase orders lose their link to the bills that received against them. The purchase order still exists and the bill still exists, and nothing connects the two, so a partly received order reads as fully open. Anyone working from that list will order the same goods twice.

Estimates change status on the way across. Active estimates arrive closed. Inactive estimates arrive rejected. If the business quotes work and then invoices against the quote, its entire open pipeline now reads as finished. Re-open the ones that are genuinely live before somebody uses the list to forecast.

Check 6: A/R and A/P aging

Run both agings and tie the totals to accounts receivable and accounts payable on the balance sheet. They should match exactly.

When they do not, the usual cause is that the Desktop file used more than one receivable or payable account and QuickBooks Online allows one default of each. Balances from the others have gone somewhere, and finding where is easier now than after a month of new transactions has been posted on top.

While the aging is open, check that credit limits, customer types and payment terms are still set the way the business relies on. None of those convert. None of them affect a balance. All of them affect what happens the next time somebody raises an invoice.

Then lock it

Once the six checks pass, set the closing date in QuickBooks Online as of the migration date. The closing date password does carry across from Desktop, so it may already be set, and it may be set to a date that no longer means anything.

Locking the period is what stops the migrated balances being edited by accident in month two and turning a settled question back into an open one.

When the checks do not pass

A migration that lands badly is not usually one catastrophic failure. It is a file that was already drifting, moved into a system that surfaces the drift.

If the trial balance comparison shows differences the three known causes do not explain, the months underneath are the problem and they are priced by how many of them need correcting:

$99per month of backlog20% off 6+ months

A file that was never right in Desktop does not become right in QuickBooks Online. Cleanup covers correcting months that exist and are wrong, catch-up covers months that were never entered, and the four checks that tell them apart take about ten minutes in the file. If you want the migration itself handled alongside the correction, that is on the migration page.