Development of non-destructive analysis systems at the R&D beamline of the Proton Accelerator Facility of the Turkish Energy, Nuclear and Minerals Research Agency (TENMAK-PAF) is described in this work. The proton beam from the cyclotron with energy between 15–30 MeV and current between 0.1 μA–1.2 mA is modified with several components and subsystems to be suitable for the application of non-destructive analysis methods. Certified reference materials (CRM) and samples with different properties were irradiated under vacuum in the irradiation chamber with the new system. Particle Induced X-ray Emission (PIXE) and Particle Induced Gamma ray Emission (PIGE) spectra of these samples were obtained with appropriate radiation detectors and measurement systems. The results of PIXE analyses and X-ray fluorescence (XRF) spectrometry were compared. PIXE and PIGE results are in good agreement with the certified values for the CRMs. This work constitutes the first reported application of non-destructive ion beam analysis methods in TENMAK-PAF and in Türkiye.