FreeAgent can be difficult to use in a multi-currency environment (EUR/GBP). Transfers between internal bank accounts are sometimes treated as income or expenses rather than simple internal transfers, which can distort revenue figures and complicate reconciliations. Currency revaluation entries may also appear directly in bank accounts, making the accounts harder to understand and audit.

In addition, subscription billing practices can be confusing, with payment attempts sometimes made across multiple stored cards. There are also concerns about how payment details are retained and managed under GDPR.

Overall, while FreeAgent may work for simple single-currency businesses, companies operating with multiple currencies or international transactions may find the system unnecessarily complex and time-consuming to manage.