Ecommerce Bookkeeping: Convert Stripe, Shopify and Square Statements

Why doesn't my Stripe payout match my sales?

Because the processor takes its fee before it pays you. A customer pays 500 dollars, the processor keeps its cut, and the deposit that reaches your bank is smaller. One deposit also usually covers many sales at once, net of refunds and chargebacks that happened in the same window. So there is no invoice anywhere in your books that matches that bank line, and there never will be.

This is the single most common reason ecommerce books are wrong, and it is not a small error. If you record the deposit as revenue, you understate sales by the amount of the fees and you record no processing expense at all. Both numbers are wrong, your gross margin is wrong, and at tax time you have understated a deductible expense. The statement the processor produces is the document that carries the missing detail.

What document does each platform actually give you?

This trips people up more than it should, because the platforms use different words for the same thing and not all of them produce something called a statement. Here is what you can actually download today, and which converter page covers each one.

Whichever document you end up with, the workflow is the same. Download the PDF, upload it to the converter at the top of this page, check the totals against the summary the platform printed, and export OFX, CSV or Excel for your accounting system.

How do I record processor fees in QuickBooks?

Record the gross sale as income and the processing fee as a separate expense, so that gross minus fee equals the net deposit that actually hit your bank. Most bookkeepers do this through a clearing account: sales post into a Stripe or Shopify clearing account at gross, fees come out of it as an expense, and the payout transfers the remaining balance to the bank account where it matches the real deposit exactly.

The clearing account is worth the small amount of extra setup because it gives you somewhere for timing differences to sit. Money a customer paid on the last day of the month but that was not paid out until the third of the next month has to live somewhere, and a clearing account is that somewhere. Without it, every month end produces an unexplained difference that someone has to chase.

Do I need a sync app or a statement converter?

They solve overlapping problems in different ways, and plenty of firms end up using both. A sync app connects to the live account through an API and posts transactions continuously. A statement converter works from the document the platform produced, which means it needs no access to the account at all.

The honest summary is that a sync app is the better tool for the current month on an account you can connect, and a converter is the better tool for everything else. Firms taking on new ecommerce clients hit the second case constantly, because the first job on a new client is almost always historical.

Can I convert a whole year of statements at once?

Yes. Bulk upload of up to 50 files in a single batch is a Plus plan feature, which covers a full year across several platforms in one pass. Files can be up to 50 MB each, and documents belonging to the same account can be merged into one extraction so twelve monthly PDFs come out as one continuous set of rows rather than twelve separate files to stitch together.

Keep one account per export. A combined export that mixes a Stripe balance and a Shopify payout account into one file will import, but the running balance in each register will jump in ways that are unpleasant to unwind later. One platform, one account, one file.

What formats can I export, and what will not work?

Exports are OFX, CSV and Excel on paid plans. OFX is the right choice for Xero and NetSuite, which both accept it. QuickBooks Online takes the CSV or OFX file directly; QuickBooks Desktop Web Connect only reads a bank issued QBO, which no converter can produce. CSV is the most flexible and the one to reach for when you want to review and recategorize before anything touches the ledger.

Two limits are worth stating plainly so nobody wastes a trial. The input has to be the statement document itself: PDF, JPG, PNG, BMP, HEIC, TIFF or TXT. CSV and Excel are not accepted as inputs, so if your platform only gave you a CSV, you already have structured data and do not need this step. And there is no QFX or QIF export. A genuine QFX carries a bank issued INTU.BID identifier that no third party can mint, which is why renaming an OFX file to .qfx always fails. If Quicken is the destination, the route that works is CSV, through File, then File Import, then Banking Transactions, then From (.CSV) File. Be aware that a Quicken CSV import does not check for or match existing transactions, so reimporting an overlapping period adds every row a second time.

Where this fits in a month end close

For an ecommerce business the close has one extra step compared to a service business, and it is this one. Bank feeds bring in the payouts, but a payout on its own tells you nothing about what was sold, what was refunded, or what the platform charged. Converting the processor statement is what turns a single deposit line into the sales, fees and refunds behind it.

Sellers running more than one channel feel this hardest. A store on Shopify taking card payments through Shopify Payments, some sales through PayPal, a market stall on Square and a marketplace listing on eBay produces four separate sets of documents, four fee structures and four payout schedules, none of which line up. Doing that by hand is where most of the month goes. If a catch up or cleanup is what you are facing rather than a routine month, the bookkeeping cleanup converter covers that workflow specifically, and the bulk bank statement converter page covers batching in more detail.