Reconcile TaxDome Payments in QuickBooks Online

When clients pay online, a transaction fee is deducted and the remaining funds are temporarily held before transferring them to your bank. Even though the money is yours when the client pays, the deposit may arrive later (e.g., paid Dec 31, deposited Jan 1), so you must record the income in the correct period.

You can reconcile TaxDome Payments in QuickBooks Online in two ways:

• Automatic payout sync (recommended for US firms): each Stripe payout posts to QuickBooks Online as one deposit that matches your bank feed
• Manual reconciliation with a clearing account : payments post to a clearing account one by one, and you record each payout as a transfer

Note

This article applies to firms using QuickBooks Online. If your firm uses QuickBooks Desktop, Xero, Wave, FreshBooks, Sage, or a similar platform, see Reconcile TaxDome Payments with your accounting software instead.

Before you start: set up invoice sync

Invoices sync to QuickBooks Online the same way whichever payment sync option you choose, so set this up first:

1. Go to Settings > Integrations from the left menu bar, then select the QuickBooks tab.

2. In the Invoice sync section, set Service income account to your income account. If you leave it empty, invoice line items sync to QuickBooks Online under the Sales service.

3. Click Save.

Note

If the payment technology fee is enabled for your firm, you’ll also select a separate Technology fee (income) account in the Payment sync section. It must be different from your Service income account.

Automatic payout sync

TaxDome Payments can sync each Stripe payout to QuickBooks Online as a single deposit, so you don’t need a clearing account or manual transfers.

Note

Automatic payout sync is available to US firms using TaxDome Payments, and your QuickBooks Online company needs an active Undeposited Funds account. Only firm owners and admins can change this setting.

To turn it on:

1. Go to Settings > Integrations from the left menu bar, then select the QuickBooks tab.

2. In the Payment sync section, select Sync one deposit per payout.

3. Under Accounts, set:

   • Processing fees (expense): the expense account for Stripe processing fees, disputes and other adjustments
   • Online payments: the bank account your payouts are deposited to
   • Manually created payments (optional): the account for offline payments
   • Technology fee (income): the income account for the payment technology fee , if you charge one

4. Click Save.

How payout sync works

Once Sync one deposit per payout is on:

• Online payments and refunds wait in Undeposited Funds, then post as one deposit per payout, linked to their existing QuickBooks Online records so nothing posts twice
• Processing fees, technology fees and technology fee reversals post as one total line each per payout
• Manually created payments keep their own account and stay out of payout reconciliation
• Billing > Payouts shows each payout’s sync status (Synced, Syncing, Not synced, Failed or Skipped)—hover over it to see why
• Payout, technology fee and processing fee errors appear on the Payouts tab of QuickBooks errors, where you can resync or skip them

Timing and changes

• Only paid payouts that arrive after you turn the option on are synced
• Negative payouts need manual handling in QuickBooks Online
• Account mapping changes apply to new deposits only
• Turning the option off keeps existing deposits; new payouts sync payment by payment again
• A reversal of an earlier payout stays out of the deposit and is listed in the deposit memo as “Not deposited—reversed payouts, handle manually”; record it in QuickBooks Online yourself
• A payment the bank takes back after payout stays out of the deposit and is listed in the deposit memo as “Not deposited—payments the bank took back”; the invoice reopens in TaxDome automatically, so there’s nothing to record in QuickBooks Online

Tip

To see which payments a payout includes, click its payout ID on Billing > Payouts. This opens Billing > Payments filtered to that payout.

Example: how a payout becomes a deposit

Here’s how one payout moves through TaxDome, QuickBooks Online and your bank. The amounts are an example.

Here’s how this deposit looks in QuickBooks Online:

Recover from a pre-activation sync error

If you had an Online payments account set before turning on Sync one deposit per payout, your first payout can include payments that synced to that account instead of Undeposited Funds, so QuickBooks Online rejects the deposit.

To fix a payout stuck in this state:

1. Open the payout’s payments: click the payout ID in the payout sync failed email, or in QuickBooks errors > Payouts under Settings > Integrations > QuickBooks.

2. Find the payments that synced to QuickBooks before you turned on Sync one deposit per payout—usually the ones dated before that day.

3. For each one, open the row’s three-dots menu and select Undo QuickBooks sync. This removes the payment from QuickBooks Online along with its processing-fee expense.

4. From the same menu, select Sync to QuickBooks. The payment is now created in Undeposited Funds.

5. Once every affected payment is re-synced, go to Settings > Integrations > QuickBooks. In QuickBooks errors > Payouts, find the payout, set Action to Resync, then click Submit.

Important

Resync the payout only after every affected payment has been unsynced and re-synced. Resyncing first fails again—QuickBooks Online still expects a document that no longer exists.

This only affects payouts that straddle the activation boundary—payouts made up entirely of payments synced after activation go through with no manual steps.

Manual reconciliation with a clearing account

If you keep the default Sync payments, refunds, and fees separately option, create a clearing account for funds TaxDome Payments is holding. This ensures your recorded payments match the actual bank deposits after transaction fees are deducted.

Step 1: Add bank payment account in QuickBooks Online

Create a dedicated clearing account in QuickBooks Online to represent funds TaxDome Payments is holding:

1. In QuickBooks Online, click the gear icon at the top right corner, and select Chart of accounts.

2. Click New account.

3. Create a checking account named TaxDome Payments Clearing.

4. Click Save and close.

Tip

Use a dedicated account instead of Undeposited Funds to simplify monthly reconciliation.

Step 2: Set up expenses for processing fees

This can be done only by a firm owner or admin :

1. Go to Settings > Integrations from the left menu bar, then select the QuickBooks tab.

2. In the Payment sync section, under Processing fee, toggle on Create Expense for Processing Fees.

Note

This expense only covers your payment provider’s own processing fee—not the payment technology fee . To sync the technology fee to QuickBooks Online, record it as income instead.

3. In the fields that appear below the toggle:

   a. Set Expense payments (clearing) to the clearing account you created in step 1 (e.g., TaxDome Payments Clearing).

   b. Set Processing fees (expense) to your chosen expense account—either Commissions & fees or a dedicated TaxDome Payments Processing Expense account.

Tip

To create a dedicated expense account in QuickBooks Online, go to Chart of accounts > New account, set the type to Expenses and the detail type to Other Miscellaneous Service Cost, and name it TaxDome Payments Processing Expense.

4. Click Save.

Step 3: Set deposit accounts

Online payments need to land in your clearing account, not straight in your bank account. Stripe holds the money for a few days and pays it out net of fees, so the clearing account shows what’s still on its way to your bank. When the payout arrives, you move it to your bank account with a transfer . If you don’t set a deposit account, payments go to Undeposited Funds.

1. In the Payment sync section, under Deposit accounts, toggle on Define “Deposit to” account for payments.

2. Set Online payments to your clearing account (e.g., TaxDome Payments Clearing).

3. Optionally, set Manually created payments to the account for offline payments .

By default, the payment technology fee isn’t recorded as a separate line in QuickBooks Online—only the invoice amount syncs. To give the fee its own place in your books, record it as income on a dedicated QuickBooks account:

4. Set Technology fee (income) to your chosen Income or Other Income account—either one you already use or a dedicated TaxDome Payments Technology Fee Income account. The account must be different from your Online payments, Manually created payments and Service income account. TaxDome doesn’t create QuickBooks accounts automatically, so choose an existing one.

Note

Technology fee (income) only appears once the payment technology fee is enabled for your firm, and this setting is off by default.

5. Click Save.

Once Technology fee (income) is set, each payment with a technology fee posts a separate, non-taxable income transaction to the configured account, using the same deposit account as the payment—the invoice amount and the QuickBooks Payment itself stay unchanged. If a payment is refunded, the corresponding portion of the technology fee is reversed on the same income account, proportional to the refund amount.

Step 4: Record Stripe payouts as transfers

When Stripe deposits funds into your bank account:

1. In QuickBooks Online, create a transfer from TaxDome Payments Clearing to your actual bank account.

2. Enter the payout amount from your bank statement.

Tip

Set up a bank rule in QuickBooks Online to automatically categorize these transfers each time.

How Stripe fees show up in QuickBooks Online

Once done, you will find your Stripe transaction fees for online payments in QuickBooks Online.

1. Go to Expenses & Bills > Expense transactions.

2. Click on an expense transaction to view the details.

You will see the Expense payments (clearing) account you configured in step 2 (e.g., TaxDome Payments Clearing) displayed as the Payment account, and the Processing fees (expense) category (e.g., TaxDome Payments Processing Expense) displayed as the Category in the QuickBooks Online expense details.

The TaxDome Payments Clearing account balance will be net of fees, matching what TaxDome Payments deposits to your operating account.

Handle offline payments

Offline payments—such as cash, check or external card terminal payments—use a separate deposit account from online payments, so they don’t mix with whatever you’ve set as your Online payments account:

1. Go to Settings > Integrations from the left menu bar, then select the QuickBooks tab.

2. In the Payment sync section, under Deposit accounts (or Accounts if you use automatic payout sync), set Manually created payments to Undeposited Funds or another account you use to track manually recorded deposits.

3. Click Save.

If you leave Manually created payments empty, offline payments go to Undeposited Funds.

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