The spaceflight storage of seeds is known to cause mutations affecting both their quality and the mature plants originating from them. To study the effects of space stress, tomato seeds of two cultivars (Lotus and Autumn rhapsody) were subjected to half a year of storage at the International Space Station (ISS), and then, sown in a greenhouse to produce tomato fruits. The space-treated plants gave smaller fruits with a stable total yield not significantly different from that of the control plants. Space-treated tomatoes showed significantly higher levels of dry matter, dietary fiber, monosaccharides and citric and malic acids and lower values of oxalic acid compared to the control plants. The pulp of space-treated fruits had 1.44–1.70 times lower levels of carotenoids, while their peel contained a 1.27–1.90 times higher pigment amount compared to the control plants. No significant changes in the total antioxidant activity (AOA), photosynthetic pigments and phenolic (TP) and proline content were recorded in the fruits due to seed spaceflight storage. Contrarily, space-treated tomatoes showed decreased levels of Ca, Sr and Mo and increased Se both in the fruit pulp and peel. The concentration of Fe and especially Pb was lower in space-treated fruit pulp. Positive correlations between Se and dry matter, Ca and Sr, Ca and Co, Ca and Fe, and Cr and carotenoids, and negative correlations between Se and Mo, Se and K, and Mo and dry matter were recorded. The results indicate that seed stress caused by long-term spaceflight affects both the biochemical characteristics and mineral composition of tomato fruits and causes the peel/pulp redistribution of carotenoids as well as macro- and micro-elements, improving Se accumulation levels in the fruit peel.