Set up the PayPal API and enable automatic feeds

This article explains how to set up your PayPal Business account to synchronise with your FreeAgent account and enable Express Checkout for receiving invoice payments online.

If you have a PayPal Business account you can accept online payments from your clients using Express Checkout and, with API access enabled, automatically sync PayPal with your FreeAgent account.

Before following the steps below, please ensure that you have confirmed your email address with PayPal.

Paypal API setup

Begin by adding your PayPal email address to your list of verified sender emails in FreeAgent. Next, add your PayPal account to FreeAgent. 

Log in to your PayPal Business account, select the 'Activity' tab and choose 'API Access' from the drop-down menu.


Select the 'Grant API Permission' link:


On the 'Add New Third Party Permissions' screen, enter and select 'Lookup':


Select the following five options from the resulting screen:

  • Use Express Checkout to process payments
  • Obtain your PayPal account balance
  • Obtain information about a single transaction
  • Search your transactions for items that match specific criteria and display the results
  • Generate consolidated reports for all accounts


Enabling an automatic feed in FreeAgent

Navigate to the 'Banking' tab at the top of the screen and select 'Bank Accounts' from the drop-down menu.

Bank Accounts.png

Choose your PayPal account from the list of accounts.


Select 'Edit Details'.


In the 'Additional Features for Business accounts' section, select from the 'Enable Automatic Feeds' and 'Enable Express Checkout' options.

We recommend that you tick the ‘Guess bank transactions’ tick box as this will ensure that the PayPal fees are split out and explained automatically for you.


What happens next?

Once the PayPal feed is enabled, the first import will be run overnight so your transactions won’t appear in FreeAgent straight away.

If there are no existing transactions in your PayPal bank account in FreeAgent, the feed will automatically import all transactions from one month ago to date when it runs overnight. However, if there are existing transactions in your PayPal bank account in FreeAgent, the feed will only begin importing transactions from 14 days before the last transaction that was either manually added or uploaded from a statement.

For example, if the last transaction in the PayPal account was dated 28th May 2024 and you enabled the API connection on 30th May 2024, the feed would import transactions from 14th May 2024 rather than for the last month, as this is 14 days before the last existing transaction. The import should filter out any existing transactions within this period to ensure duplicates are not created.

If you need to import historical transactions that are outside the scope of the PayPal feed, you will need to either upload bank statements or enter transactions manually.

Foreign currency transactions

FreeAgent can account for any income you receive through foreign currency PayPal transactions.

If you’ve set up your PayPal account to automatically convert foreign currency transactions into your FreeAgent base currency*, you should set up a single PayPal account in FreeAgent in that currency. Your converted transactions will then import and will be posted to your accounts as normal.

If you hold multiple foreign currency balances in PayPal, you'll need to set up separate accounts in FreeAgent (one for each currency) and choose the appropriate currency when you complete the details for each account.


FreeAgent will only import PayPal transactions that are in the relevant currency for each of your PayPal accounts in FreeAgent, so all your foreign currency transactions will feed through to their respective accounts separately.

How FreeAgent accounts for foreign currency transactions

FreeAgent automatically accounts for your foreign currency PayPal transactions in the base currency of your FreeAgent account, using the latest exchange rate on

This means that the figures on your accounting reports (such as your balance sheet and profit and loss report), and the figures you see on your overview screen will be displayed in your base currency. FreeAgent revalues your accounts every day against the current exchange rate and updates your converted figures accordingly.

*If you have a UK account, your base currency will be GBP, if you have a US FreeAgent account, it will be US dollars, and if you have a Universal account, it will be the currency you selected when you first set up your FreeAgent account.

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