It is always better to follow the industry's best approach to avoid the reconciliation nightmare.
Follow the steps to Reconcile Stripe Payments in QuickBooks Online
Step 1: Create a Bank Account named "Stripe Bank Account" (or name it as needed) in QuickBooks Online. This account will be used to record your Stripe sales & Stripe fees.
2: CHECKING ACCOUNT/CURRENT ACCOUNT should not be used directly to record your Stripe sales as it will create numerous issues in reconciling the Stripe fees.
Step 1: Connect PayTraQer with your QuickBooks Online (How to?)
Step 3: Configure the sync settings for Sales, Expense, Fees, Items & Payout (How to?)
Step 4: Record ( Sync) the transactions from Stripe to QuickBooks Online (How to?)
While providing the settings, you need to select the same bank account ("Stripe Bank Account" or created Bank Account) for Sales, Expense, Fees, Items & Payout.
Configure Stripe Sales settings with your Stripe Bank Account
Configure Stripe Fees settings with your Stripe Bank Account
Configure Stripe Expenses settings with your Stripe Bank Account
Configure Stripe Payout settings with your sales account
Step 3: QuickBooks Online Bank Review
Step 1: Navigate to the Banking Section in QuickBooks Online, you could see that the TRANSFER transactions of "Stripe Bank Account" is matched against your deposits. These TRANSFER transactions won't be created if you have not enabled Payout processing in PayTraQer.
Step 2: Click the "Match" link to accept the transactions.
You can also create TRANSFER transactions directly in the Bank Review screen if it is not available.
Step 4: QuickBooks Online Reconciliation
Step 1: Navigate to the bank reconciliation page in QuickBooks Online.
Step 2: Provide a statement balance amount and statement date.
Step 3: Start the Reconciliation Process.
QuickBooks Online automatically matches the transfers and deposits and marks the transactions as reconciled. Now QuickBooks Online Stripe sales ( Invoices, Sales Receipts) and Stripe Expenses ( Fees, Expenses) are properly matched with your checking account.