NGOs that use financial means for their activities must be subjected to financial management regulations. These regulations include international accountancy principles as well as current legislation in force in Kosovo. Each registered NGO must have a bank account and must receive any and all of the funds only through the bank. Also, the aim should be set so that all payments made by the CSO are carried out through bank transfer, except for small expenditures which are impossible to be carried out through bank transfer. All payments must be made based on regular bills or contracts for services, whereas each payment must be authorized by the Executive Director and the Financial Manager. Accountancy ledgers must be kept for all financial transactions, whereas the organization is obliged to produce regular reports on income and payments (at least once a year).

Organizations that have a Public Beneficiary status with an annual turnover of over 100,000 EUR are obliged to be subjected to annual audits by independent certified auditors. Also it is preferred that organizations that do not enjoy a Public Beneficiary Status also carry out regular audits of projects and of the overall organization.