Purpose The study of mechanisms of plant responses to extreme conditions, particularly, microgravity and ionizing radiation, is crucial for space exploration. Modern space biology of plants focuses on increasing plant tolerance to harsh conditions of space environment. Given the limited access to the International Space Station, we designed and assembled the 3D clinostat for mimicking microgravity, which, in combination with proton irradiation, allows simulating space conditions. As a case study for testing the device, we studied the effect of clinostating on Arabidopsis thaliana accession originating from the Chernobyl exclusion zone. Materials and Methods Using the combined clinostating and proton irradiation, we simulated the conditions of long-term space flight for Arabidopsis thaliana plants of the Chernobyl accession – progeny of chronically irradiated plants, grown from field-collected (Masa-0) and laboratory-cultivated (Masa-0-1) seeds, and for wild-type Col-8. The clinostating and irradiation of plants were also carried out separately. Plant responses were studied as photosynthetic and phenotypic endpoints of seedlings. Results and Conclusions Parameters of chlorophyll fluorescence estimated immediately after exposure showed that Masa-0-1 plants were resistant to the simulated space conditions, while Masa-0 demonstrated modulation of non-photochemical fluorescence quenching. Proton irradiation generally inhibited photosynthesis of Masa-0, Masa-0-1, and Col-8 seedlings. The combined effect of irradiation and clinostating modulated the photosynthetic activity of Col-8 seedlings. The leaf area of seedlings did not change after exposure to simulated conditions. The 3D clinostat model and software are published along with this article for researchers interested in the field of space biology.