The public higher education system in the Republic of Kosovo faces big challenges. One essential part is ensuring the effective use of public funding. In this context the European Union-funded TEMPUS project “Increasing the Financial Autonomy and Accountability at Public Higher Education Institutions in Kosova”has given an important impulse. During the last 3 years the focus has been on the modernisation of the financial management practice, including the comprehensive training of the universities’ administrative staff.