The Educational Irish Research Satellite (EIRSAT-1) is a 2U CubeSat developed at University College Dublin. The project aims to build, test, launch, and operate Ireland’s first satellite and to perform in-orbit demonstrations of three novel payloads developed in-house. To reduce risk within the mission, the project employs a prototype model philosophy in which two models of the spacecraft exist: an engineering qualification model (EQM) and a flight model (FM). This paper presents the verification approach of the functional tests implemented for the EIRSAT-1 project. The activities of the FlatSat and system level full functional tests of the EQM are presented and the results obtained during the test campaigns are discussed. Four test anomalies were encountered during the full functional test campaign resulting in two minor redesigns, and subsequent reassembly, of the CubeSat. The functional test campaigns highlighted the importance of FlatSat level testing of CubeSats to ensure compatibility of all subsystems prior to assembly and of thorough documentation to diagnose any unexpected behaviour of the hardware efficiently. The functional verification of the EQM proved that the system conformed to its design, verifying 57 mission requirements, and is a crucial step towards the development of the EIRSAT-1 FM.