Future space missions will include return to the Moon and long duration deep space roundtrip missions to Mars. Leaving the protection that Low Earth Orbit provides will unavoidably expose astronauts to higher cumulative doses of space radiation, in addition to other stressors, e.g. microgravity. Immune regulation is known to be impacted and it remains to be seen whether prolonged effects will be encountered in deep space that can have an adverse impact on health. In this study we investigated the effects in overall metabolism of three different low dose radiation exposures (γ-rays, 16O, and 56Fe) in spleen from male C57BL/6 mice at 1, 2, and 4 months after exposure. Forty metabolites were identified with significant enrichment in purine metabolism, tricarboxylic acid cycle, fatty acids, acylcarnitines, and amino acids. Early perturbations were more prominent in the γ irradiated samples, while longer term responses shifted towards the high energy particle effects. Regression analysis showed a positive correlation of fatty acids with time and negative association with γ-rays, while degradation of purines were positively associated with time. Taken together, there is a strong suggestion of mitochondrial implication and the possibility of long term effects in DNA repair and nucleotide pools following radiation exposure.