This paper explains the architectural designs of the institutional repositories which are parts of Slovenian open access infrastructure and the challenges we had to deal with during the setting-up. Rules and processes for mandatory submissions of final study works, research data and research publications were established during the setting up of institutional repositories. An important aspect of this implementation was the support of Slovenian institutions management and good cooperation with librarians and IT professionals. Compared to establishing several repositories for individual departments or academies of each university or research institution, the proposed solution with a common institutional repository is more effective from the financial and time aspects as well as the human resources perspectives. Institutional repositories exchange data with the national bibliographic system COBISS.SI, Slovenian current research information system SICRIS, university information systems, and national open access infrastructure. The features unused in well-known open source solutions of institutional repositories are mentor statistics, automatic document segmentation, name authority control with CONOR.SI authority file and availability of institutional repositories from mobile applications for Android, Windows Phone, and iOS devices.