Software and migrations
Stripe and Shopify integration
Stripe and Shopify payouts bundle gross sales, processing fees, refunds and chargebacks into one deposit that hides the real fee load. Finbryn connects both to QuickBooks Online or Xero so each component posts separately and daily or weekly payouts reconcile to processor statements.
Migration checklist
Illustrative client · August 2026
USD
- Old file backed up with full historyDone
- Chart of accounts mapped line by lineDone
- Opening balances agreed to the old fileDone
- Bank feeds connected and testedIn progress
- First month closed in the new softwareNext
Illustrative. An example of the document, not a client's figures.
Why one deposit line is not enough
A Stripe or Shopify payout is a net number: gross sales minus processing fees, refunds and chargebacks, sometimes minus a rolling reserve on top. Booking that net deposit as revenue understates both sales and expenses for the period and makes it impossible to see the real processing cost as a percentage of revenue. Most US ecommerce and SaaS businesses running card payments hit this problem within the first few months of live transactions.
What setup covers
We connect Stripe and Shopify Payments to QuickBooks Online or Xero, often through A2X for higher-volume Shopify sellers, and map the chart of accounts so gross sales, processing fees, refunds and chargebacks each land in their own account. Daily or weekly payouts get reconciled against the processor's own settlement reports so the bank deposit always ties back to a documented breakdown rather than an assumption.
Sales tax collected through Shopify
Shopify collects and, in most states, remits sales tax on a seller's behalf as a marketplace or platform facilitator, but that collected tax still needs to post to a liability account rather than get swept into revenue. We review Shopify's tax settings against the states where a seller has economic nexus and confirm the mapping is set up correctly before it compounds across a full year of transactions.
Clearing a backlog
Many businesses arrive with months of net deposits already sitting in QuickBooks or Xero as unreconciled income. We rebuild those historical periods into their real components, gross sales, fees, refunds, so trailing reports are not permanently overstating revenue and understating cost.
Questions
Frequently asked questions: Stripe and Shopify integration
Should I record my Stripe or Shopify payout as one deposit?
No. A single deposit line hides processing fees and refunds, which understates expenses and overstates net revenue for the period. We break each payout into its components before it posts.
Do you connect Stripe directly or only through Shopify?
Both. Stripe connects directly for businesses billing outside Shopify, such as SaaS subscriptions, and through Shopify Payments for ecommerce sellers, often paired with A2X for higher transaction volume.
Does Shopify's sales tax collection mean I don't need to think about nexus?
No. Shopify collecting and remitting tax as a facilitator does not remove your own economic nexus obligations in every state; we confirm the mapping matches where you actually have nexus.
What does stripe and Shopify integration actually include, month to month?
Stripe and Shopify integration covers stripe and Shopify accounts connected to QuickBooks Online or Xero, along with chart of accounts mapped for gross sales, processing fees, refunds and chargebacks. The work runs inside Stripe, Shopify, A2X, QuickBooks Online or Xero, the file stays under your own subscription, and a senior principal reviews the output before it reaches you each period.
What access do you need to start stripe and Shopify integration?
View or edit access to Stripe, Shopify, A2X, QuickBooks Online or Xero is enough to begin; nothing about your existing subscription or login changes on our side. Any additional access needed for a specific deliverable, such as a bank portal or receipt inbox, is agreed with you first, and the scope is set out in your engagement letter.
Should Stripe payouts be recorded as one deposit or broken out?
Broken out. A single deposit line hides fees and refunds, which understates expenses and overstates net revenue for the period.
Do you handle Shopify Payments as well as Stripe directly?
Yes, both route through the same reconciliation process once connected.
What software works with stripe and Shopify integration?
Stripe and Shopify integration runs inside Stripe or Shopify, whichever you already use. If you are not yet set up in either, we can configure a file in your name so you keep ownership of it once the engagement is under way.
How do we get started with stripe and Shopify integration?
Getting started with stripe and Shopify integration begins with a short review of your current records and software access. Once that is done we confirm scope and timing in writing, and ongoing work begins on the schedule agreed with you.
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Next step
Talk to the team that would run your books
A short call covers your setup, your software and what a first month would look like. You get a written scope and price after it.