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Using Multiple Payment Gateways on Shopify? We've Got You Covered!
When selling through Shopify, you can choose to accept payments via Shopify Payments or a wide variety of other payment gateways like PayPal, Klarna, Stripe, and more.
The good news? Link My Books supports all Shopify payment gateways.
No matter which ones you're using, we'll automatically handle them for you.
⚙️ Deactivation of Payment GatewaysAll available payment gateways will be activated by default when you connect your Shopify store to Link My Books.
Want to exclude some? Just head to:
Settings > Settlement Settings and untick any gateways you don't want us to create summary invoices for.
📦 How Do Payment Gateways Work in Link My Books?
For each active payment gateway, we create a monthly summary invoice for every currency you've received payments in.
Example:
If you use PayPal and accept payments in both GBP and USD, Link My Books will create:
1 summary invoice per month for GBP PayPal sales
1 summary invoice per month for USD PayPal sales
It's that simple.
🧾 Automatic Clearing Accounts for Each Gateway
Every payment gateway you use will have its own clearing account automatically created in your chart of accounts.
This helps make reconciling your payment gateway sales much easier.
Need a deeper dive into how this works? Check out our article on clearing accounts and reconciliation.
📊 Gateway Clearing Account Balance Building Up on Your Balance Sheet?
If you notice that a gateway clearing account (e.g. "Shopify Gateway Clearing", "PayPal Gateway Clearing", or "Klarna Gateway Clearing") has a growing balance on your balance sheet, this usually means that one side of the clearing account is missing transactions.
How clearing accounts work: When Link My Books posts a settlement for a payment gateway, it creates a debit entry in the clearing account (representing the sales processed through that gateway). When you reconcile the actual payout from the payment provider in your bank feed, that creates a credit entry against the same clearing account. Over time, these debits and credits should net off to zero (or close to it).
If the balance is building up, it typically means one of the following:
Bank payouts aren't being coded to the clearing account — When you receive a payout from a third-party gateway (e.g. PayPal, Klarna, Stripe) into your bank account, the bank transaction needs to be allocated against the corresponding gateway clearing account in your accounting software. If these payouts are being coded to a different account (or left unreconciled), the credit side of the clearing account will be missing and the balance will grow.
Timing differences — There may be a delay between when Link My Books posts the settlement (debit) and when the actual bank payout arrives and is reconciled (credit). This is normal and usually resolves itself within a few days.
Gateway fees not accounted for — Some payment gateways deduct fees before paying out. The settlement amount posted by Link My Books reflects the gross sales, but the bank payout reflects the net amount after fees. This small difference can accumulate over time. Check your fee settings in Settings > Settlement Settings.
How to fix it:
Open the clearing account in your accounting software (Xero or QuickBooks) and review the transactions
Check whether bank payouts from the payment gateway are being coded to this clearing account — if not, re-code them
Look for any unreconciled bank transactions from the payment provider that need to be matched
If you use custom clearing account mappings, make sure the bank rule or reconciliation rule points to the correct clearing account — see our article on custom gateway clearing account mappings
⚠️ Important: This is one of the most common causes of balance sheet discrepancies for sellers using third-party payment gateways alongside Shopify Payments. The key thing to remember is that clearing accounts need both sides of the transaction — the Link My Books settlement (debit) and the bank payout reconciliation (credit) — to balance correctly.
🔧 What is the "Manual" Gateway?
You may notice a gateway labelled "Manual" (sometimes shown as "Manual; Gateway Clearing") appearing in your settlements or on your balance sheet. This is not an error — it represents orders in Shopify that were recorded with a manual payment method rather than an automated payment gateway like Shopify Payments or PayPal.
Common reasons you might see a Manual gateway entry include:
Orders marked as paid manually (e.g. cash on delivery, bank transfer, trade orders)
Draft orders created in Shopify that were marked as paid outside of a payment gateway
POS transactions processed without a connected payment terminal
How to review Manual gateway orders: Click into the settlement on your Settlements Dashboard and review the audit data. This will show you the individual order numbers included in the Manual gateway summary. You can then look up those orders in Shopify to confirm what they relate to.
Don't need the Manual gateway? If the orders in the Manual gateway don't need to be accounted for (e.g. they are internal test orders or duplicates), you can disable it by going to Settings > Settlement Settings > Shopify Payment Gateways and unticking the Manual gateway.
💡 Tip: If you see a persistent balance in the Manual Gateway Clearing account on your balance sheet, it usually means the manual orders have been recorded but no corresponding bank deposit has been allocated against them. Review the order numbers in the audit data to decide whether these need reconciling or can be disabled.
🤔 Missing Settlements from Some Gateways?
Here's the deal:
We only start pulling in transactions from the date the payment gateway was enabled.
So, if you ticked a gateway after your initial Shopify setup, we won't automatically bring in historical data for it.
Need those earlier settlements?
Just contact our support team and we'll help you out.
⚠️ A Monthly Gateway Settlement Hasn't Appeared At All?
If an entire monthly settlement for a payment gateway (e.g. PayPal for February) is missing from your dashboard — not just showing a discrepancy, but completely absent — this is different from a small amount mismatch.
What to check first:
Confirm the gateway is still enabled in your Settings > Settlement Settings > Shopify Payment Gateways tab
Check that you had orders through that gateway during the month in question by reviewing your Shopify admin
Look at the previous month's settlement for the same gateway — if that one is present, it suggests a processing issue rather than a configuration problem
If the gateway is enabled and you did have orders but the settlement is missing: This is occasionally caused by a temporary processing glitch on our end. Please contact our support team and let them know which gateway and which month is affected. Our team can reprocess the settlement for you, which typically resolves the issue within a few minutes.
⚠️ Note: If you notice a missing gateway settlement, it's worth checking your other Shopify accounts too (if you have multiple). In rare cases, a processing glitch can affect more than one account at the same time.
💬 Still Got Questions?
No worries! Our support team is always happy to help.
Just click the blue message widget in the bottom-right corner of this page and we'll get back to you ASAP.
If you have any questions about this article or feedback on how we could make it better please reach out to the support team via the blue chat icon on the bottom right of the page or via email to [email protected].