The Quipli/QBO integration is a one-way sync from Quipli → QBO. Any invoices or payments recorded in QBO will NOT be updated in Quipli. It is highly recommended to manage all payments, regardless of payment method, through Quipli and have them sync over into QBO. Processing payments through both QBO and Quipli will cause duplicate payments to appear in QBO. Additionally, any changes that need to be made to an invoice should occur within Quipli, as these changes will sync over to QBO. If changes are made to an invoice within QBO, they will not sync back to Quipli, causing discrepancies in invoice totals between QBO & Quipli.
This article covers two methods for reconciling Stripe fees in QBO: the Payout Sync (recommended) and the manual method. If you have Payout Sync enabled, follow the steps in Method 1. If not, use Method 2.
ℹ️ Feature Availability: Payout Sync must be enabled by the Quipli support team or your Customer Success Manager before you can use it. Contact [email protected] to get it turned on.
Method 1 — Payout Sync (Recommended)
Payout Sync automates the reconciliation process by syncing each Stripe payout directly to QuickBooks as a single deposit with Stripe fees handled automatically.
Prerequisites
Before syncing a payout, make sure you have mapped both of the following accounts in your Quipli QBO settings:
QuickBooks bank account — the checking account where Stripe deposits land
Stripe fees expense account — an expense account (Detail Type: Bank Charges) to record Stripe charges against
Reference QBO Integration Setup for how to map these accounts.
Step 1 — Review Your Payouts
In Quipli, go to Accounting → Payout Reconciliation.
Each payout in the list displays: total payments collected, refunds, Stripe fees, and net deposit amount.
Click on any payout to expand it and see the individual payments that make it up.
Step 2 — Sync a Payout to QuickBooks
On any payout, click Sync QBO.
Quipli will:
Batch all individually synced payments into a single deposit
Automatically create a separate expense entry for Stripe fees
Set the total deposit amount to match your actual bank deposit
📌 Ongoing Syncs: The first sync for each payout is manual. After that, all subsequent payouts sync automatically on a daily basis. You can still trigger a manual sync at any time if a payout doesn't appear in QuickBooks.
Step 3 — Match in QuickBooks Bank Feed
In QuickBooks, go to Bank Transactions.
Find the deposit in your bank feed. QuickBooks will suggest a match — the Quipli deposit you just synced.
Click Match. Done.
Method 2 — Manual Reconciliation
If you do not have Payout Sync enabled, use this method to manually reconcile Stripe fees in QBO. The process varies slightly depending on whether your bank account is linked directly to QBO.
Setup
Within QBO: Make sure you have selected a default payment account in your Quipli settings. We recommend using an Undeposited Funds account (Detail Type: Undeposited Funds) as a temporary holding account until funds clear and are deposited to your checking account. Also create one additional account:
Stripe Charges (Expense Account, Detail Type: Bank Charges)
Within Quipli: Go to Accounting → Payout Reconciliation and click on the desired payout. You will see a summary of payments received, refunds, Stripe fees, and the net deposit amount. Below the summary is a list of each individual payment in the payout, showing the gross amount paid by each customer and the Stripe fee deducted.
Use this information to calculate total Stripe charges for a given day or period, and verify the expected payout amount.
If your bank account is NOT linked directly to QBO
Payments synced from Quipli will record to Undeposited Funds in QBO at the full customer-paid amount.
Once you have the total expected payout amount, record a Deposit from Undeposited Funds to your checking account. (Reference: Record and Make Bank Deposits in QBO.)
In the Add funds to this deposit section at the bottom of the Deposit screen, enter the total Stripe fees as a negative amount and code it to the Stripe Charges expense account.
Complete the deposit. The total will now match your actual bank deposit.
If your bank account IS linked directly to QBO
Stripe payouts will appear automatically in your QBO bank feed. To avoid a duplicate deposit, you need to match the individual Quipli payments to the bank transaction rather than creating a new deposit.
In the bank feed, find the Stripe payout and use the Find more matches option to select the Quipli payments that make up that payout. (Reference: Matching Online Bank Transactions in QBO.)
Toggle Resolve to On. In the Add Resolving Transactions section that appears, enter the total Stripe fees as a negative amount coded to the Stripe Charges expense account.
Complete the match process.
Need Help?
Contact Quipli support ([email protected]) if you:
Want to enable Payout Sync for your account.
Synced a payout but it isn't appearing in QuickBooks.
See a mismatch between the Quipli deposit amount and your actual bank deposit.
Are unsure how to map your bank account or Stripe fees expense account in QBO settings.