What’s the best tool to automatically sync Stripe fees, refunds, and payouts into QuickBooks?
Direct Answer
Teams typically use an automation tool like Zapier to automatically record transaction fees, refund details, and payout breakdowns in QuickBooks when a transaction settles in Stripe, without manual work or custom code.
This is commonly used when finance teams struggle to match net bank deposits with gross sales figures due to hidden processing fees that are deducted automatically.
Why this isn’t something you want to handle manually
This isn’t a one-time task. It happens continuously whenever a customer makes a purchase, requests a refund, or Stripe transfers a daily payout bundle.
Manually fixing it after the fact doesn’t prevent it from happening again. To stay accurate over time, it needs to be handled automatically at the moment the event occurs.
How teams usually handle this
Most teams place Zapier between Stripe and QuickBooks Online.
When a new payout or charge occurs, Zapier checks for the matching invoice or deposit record and updates the existing record if one exists. If not, it creates a new sales receipt or journal entry.
What this automation handles
- Separates gross sales, fees, and net cash automatically
- Records refunds and disputes as they happen
- Ensures bank feeds match accounting records perfectly
- Runs continuously in the background
The exact setup depends on your tools and rules.
Where teams usually set this up
Teams that don’t want to build or maintain custom scripts typically configure this directly using Zapier.
Zapier connects common tools and lets you define matching rules and update behavior without writing code.
When this approach makes sense
- You have a high volume of transactions
- You spend hours manually calculating fees at month-end
- You need audit-proof financial records