How does Seller Ledger handle Shopify Balance and other Shopify bank accounts?

If you sell on Shopify, you may have opened one or more of the bank accounts that Shopify offers to sellers — most notably Shopify Balance, but also related checking and savings accounts provided through their banking partner, Fifth Third Bank. These accounts can be connected to Seller Ledger just like any other bank account, but because they interact directly with your Shopify store's payouts, it's worth understanding how the pieces fit together.


What is Shopify Balance?

Shopify Balance is a business bank account offered by Shopify that's built to receive your Shopify store's payouts directly, often faster than a traditional external bank. Shopify also offers additional accounts — such as a linked savings account — that sit alongside Shopify Balance under the same banking relationship.


From an accounting perspective, these behave like any other business bank account:


  • They have their own balance.
  • Money flows in (usually from Shopify payouts).
  • Money flows out (to pay expenses, transfer to another bank, etc.).

Shopify Balance and related nank accounts are connected to Seller Ledger the same way as any other bank account — through our banking partner, Plaid.


  1. From your dashboard, click Add Channels, Banks and Accounts.
  2. Choose Add Bank, Credit Card or PayPal.
  3. Search for your Shopify Balance / Fifth Third Bank connection and log in.
  4. Select the account(s) you want to link.

Once connected, each account will appear on your dashboard with its current balance, just like a traditional bank account.


How Shopify payouts flow into Shopify Balance

When you have your Shopify store connected to Seller Ledger, we import your Shopify order and fee details on the Shopify side, and then Shopify pays you out to whichever bank account you've designated. If that bank account is Shopify Balance, here's what you'll see:


  • On the Shopify side: each payout shows up as a withdrawal (a negative amount) from your Shopify store account in Seller Ledger.
  • On the Shopify Balance side: the same payout shows up as a deposit.

Seller Ledger automatically matches these two sides and treat them as a transfer — meaning the payout amount does not get double-counted as income. Your income was already recorded on the Shopify store side, when the orders came in.


If a payout doesn't match automatically

Sometimes Seller Ledger can't automatically match a Shopify payout to the corresponding deposit in Shopify Balance. This can happen if the two sides arrive a day or two apart, or if the amount was adjusted slightly. To fix it manually:


  1. Click into your Shopify Balance account from the dashboard.
  2. Find the uncategorized deposit.
  3. Click the yellow Uncategorized income button.
  4. Scroll to the bottom of the category list and choose Transfer: [your Shopify store name].
  5. Save.

For more on this, see Why are some of my payouts being categorized as uncategorized income?


Transfers between Shopify Balance and other Shopify accounts

Many sellers use more than one Shopify-provided account — for example, keeping most funds in Shopify Balance and sweeping a portion into a Shopify savings account, or moving money into a separate Fifth Third checking account. Whenever you move money between two accounts that are both connected to Seller Ledger, you'll see the transaction appear in both places:


  • A withdrawal from the account the money left.
  • A deposit into the account the money went to.

These should be categorized as transfers so they don't affect your profit and loss.


To categorize them:


  1. Click into either account and find the transaction.
  2. Click to categorize it.
  3. Scroll to the bottom of the category list and choose Transfer: [name of the other account].
  4. Save.

Seller Ledger will often auto-match the other side of the transfer as well. If it doesn't, just repeat the steps in the other account.


For more background on transfers, see Handling transfers between accounts.


Transfers from Shopify Balance to an outside bank

If you move money from Shopify Balance to an external bank account (for example, your primary business checking account at another bank):


  • If that outside account is also connected to Seller Ledger, categorize both sides as Transfer: [other account name]. Seller Ledger will usually match them automatically.
  • If that outside account is not connected to Seller Ledger, categorize the withdrawal from Shopify Balance as Transfer: Non-connected Account. This keeps your Shopify Balance running total accurate without treating the withdrawal as an expense.

A quick example

Let's say in a given week you have:


  1. $2,000 in Shopify sales (imported automatically on the Shopify side).
  2. A $1,850 Shopify payout deposited into Shopify Balance (after Shopify fees).
  3. A $500 transfer from Shopify Balance to a Shopify savings account.
  4. A $1,000 transfer from Shopify Balance to your outside business checking account (also connected to Seller Ledger).

Here's how each piece should be categorized in Seller Ledger:


  • The sales are already recorded on the Shopify side — no action needed.
  • The $1,850 payout shows up as a withdrawal from Shopify and a deposit in Shopify Balance. These are matched (or manually categorized) as Transfer: Shopify Balance.
  • The $500 to savings shows up in both accounts. Categorize as Transfer: Shopify Balance Savings (or whatever you named the account).
  • The $1,000 to outside checking shows up in both accounts. Categorize as Transfer: [your outside checking name].

None of these transfers affect your profit and loss — because your income was already captured when the Shopify orders came in.


A few tips

  • Don't categorize Shopify payouts as income in Shopify Balance. Doing so would double-count your revenue, since Shopify orders were already recorded as income.
  • Keep an eye out for duplicates. Fifth Third Bank has occasionally sent duplicate transactions through Plaid. If you see one, hide the duplicate rather than deleting it.
  • Use "Not for business" for personal spending. If you happen to use Shopify Balance for a personal purchase, categorize that transaction as Not for business so it stays out of your reports and taxes. See How do I handle personal transactions in a bank or credit card account? for more.

Summary

  • Shopify Balance and other Shopify-offered accounts (through Fifth Third Bank) connect to Seller Ledger via Plaid, just like any other bank account.
  • Shopify payouts appear on both the Shopify side and the Shopify Balance side, and should be treated as transfers — not income.
  • Movements between Shopify Balance and other Shopify accounts (savings, checking) should also be categorized as Transfer: [other account] on both sides.
  • If money leaves Shopify Balance to an account not connected to Seller Ledger, use Transfer: Non-connected Account.
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