The EU budget is financed almost entirely through own resources.
These funds are credited twice a month to the European Commission accounts opened with Member State treasuries or central banks. From there, the Commission transfers the necessary funds to its accounts with commercial banks, from which payments are made to EU beneficiaries.
The EU's treasury management is based on the just-in-time principle; i.e. the Commission keeps the resources collected from Member States on its accounts held with Member States. It then transfers these funds to the accounts held with commercial banks only to the extent necessary to carry out its daily payments, and so does not 'stock' funds on accounts other than those opened with Member States' institutions.