GoCardless is a direct debit payment merchant which will allow you to take payments for invoices within Clear Books. The system will mark these invoices as paid and apply the GoCardless fee automatically. 

The way this works is that you create a GoCardless Mandate with your customer which is essentially an agreed amount of money that your customer allows you to take payment for invoices from. You can then take payments, manually or automatically, from these GoCardless Mandates for any of your sales invoices. 

You can enable GoCardless on the Settings > Organisation > Configure system > Toggle features on the Features tab.

Once enabled the feature will appear on the Tools > Integrations > GoCardless menu. You will need to register with GoCardless or alternatively log in to your existing account.


When GoCardless has been successfully set up, the system will create a new bank account on the Money > Bank accounts menu (called GoCardless by default). All payments via GoCardless will be received into this bank account and the payment method will be set to Direct Debit by default. All GoCardless fees will also default to the account code Bank charges.

You can change these details on the Tools > Integrations > GoCardless > Settings menu although we recommend you use the defaults.

If you tick the option to automatically take payment requests when mandates are available, the system will search for any unpaid invoices and attempt to take payment from a mandate if available. It will also mean any invoices you create in future will attempt to take payment automatically from available mandates.


A GoCardless Mandate first needs to be agreed with your customer to allow you to take payments for invoices. The mandate limit currently defaults to £5,000 and can be requested by the CB user on the Tools > Integrations > GoCardless > Mandate  menu.

This menu also allows you to import mandates setup in GoCardess. These existing mandates can also be imported in bulk from a CSV file. 

You can also request a mandate from any unpaid invoice from the GoCardless section under the Payment history table. 

Your customer can also set up their own mandate from the customer statement. A link to the customer statement is sent out with every invoice and customer statement email. 

Requested mandates can be viewed on the Tools > Integrations > GoCardless > Mandates menu and can be re-sent or cancelled if necessary.

Accepted mandates can also be viewed on this menu and will show the total value and the amount remaining. The mandates can be cancelled using the Manage drop down field.

The total remaining will reset at the end of the month, if the full amount from the mandate is not taken this will not roll over into the next month. The month begins on the date at which the mandate was accepted by the customer.

Taking payment manually

You can take payment manually from a mandate for any invoices up to the value of the mandate limit. To do this click on any unpaid invoice on the Sales > Invoices > Unpaid menu. Under the GoCardless Payments table click on the available mandates link.

Alternatively, you can take payment from the Tools > Integrations > GoCardless > Payments menu. Use the check box to select the appropriate invoices and then click on the Use available mandates button.

In both cases the payment process begins immediately. Remember that if you would like this process to be automated you can use the Auto collect option as explained in the Settings section above.

Taking payment from recurring templates

When you create a recurring invoice template you can select GoCardless as the payment account (below the summary box at the bottom of the form) - this will pop up an option to take payment on recurrence, Attempt to collect money automatically from customer, which needs to be ticked. What this will mean is that when each invoice is recurred it will find the available mandate and take payment from it.

Make sure that the invoices are set to recur as approved and that there the Create payment on occurrence checkbox is not ticked. 

GoCardless Payments

The GoCardless payment process will take between 5-7 days. When payment is received Clear Books will automatically mark the invoice as paid, this payment will use the GoCardless bank account unless you have changed this in the settings.

The status of payments can be viewed on the Tools > Integrations > GoCardless > Payments menu. You can cancel GoCardles payments by using the Manage drop down field, however, you have up until 4pm, two working days before the charge date.

You can also view the payment status on any unpaid invoice that a payment has been triggered, under the GoCardless invoices table.

The actual money received into your business account is the invoice amount less the GoCardless transaction fee.  Make sure to explain the money received as a transfer from the GoCardless account.  

GoCardless fee

Every payment that goes via GoCardless incurs a GC fee which is 1% of the payment capped at £2 (minimum 20p). The system will generate the GC fee automatically by creating a paid bill coded to bank charges. This bill is automatically paid using the GoCardless bank account (unless you have changed this in the Settings).

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