Bone loss and immune dysregulation are among the main adverse outcomes of spaceflight challenging astronauts' health and safety. However, consequences on B‐cell development and responses are still under‐investigated. To fill this gap, we used advanced proteomics analysis of femur bone and marrow to compare mice flown for 1 mo on board the BION‐M1 biosatellite, followed or not by 1 wk of recovery on Earth, to control mice kept on Earth. Our data revealed an adverse effect on B lymphopoiesis 1 wk after landing. This phenomenon was associated with a 41% reduction of B cells in the spleen. These reductions may contribute to explain increased susceptibility to infection even if our data suggest that flown animals can mount a humoral immune response. Future studies should investigate the quality/efficiency of produced antibodies and whether longer missions worsen these immune alterations.—Tascher, G., Gerbaix, M., Maes, P., Chazarin, B., Ghislin, S., Antropova, E., Vassilieva, G., Ouzren‐Zarhloul, N., gauquelin‐Koch, G., Vico, L., Frippiat, J.‐P., Bertile, F. Analysis of femurs from mice embarked on board BION‐M1 biosatellite reveals a decrease in immune cell development, including B cells, after 1 wk of recovery on Earth. FASEB J. 33, 3772–3783 (2019). http://www.fasebj.org