Head-down bed rest (HDBR) reproduces the cardiovascular effects of microgravity. We tested the hypothesis that regular high-intensity physical exercise (JUMP) could prevent this cardiovascular deconditioning, which could be detected using seismocardiography (SCG) and ballistocardiography (BCG). 23 healthy males were exposed to 60-day HDBR: 12 in a physical exercise group (JUMP), the others in a control group (CTRL). SCG and BCG were measured during supine controlled breathing protocols. From the linear and rotational SCG/BCG signals, the integral of kinetic energy ($$iK$$
iK
) was computed on each dimension over the cardiac cycle. At the end of HDBR, BCG rotational $$iK$$
iK
and SCG transversal $$iK$$
iK
decreased similarly for all participants (− 40% and − 44%, respectively, p < 0.05), and so did orthostatic tolerance (− 58%, p < 0.01). Resting heart rate decreased in JUMP (− 10%, p < 0.01), but not in CTRL. BCG linear $$iK$$
iK
decreased in CTRL (− 50%, p < 0.05), but not in JUMP. The changes in the systolic component of BCG linear iK were correlated to those in stroke volume and VO2 max (R = 0.44 and 0.47, respectively, p < 0.05). JUMP was less affected by cardiovascular deconditioning, which could be detected by BCG in agreement with standard markers of the cardiovascular condition. This shows the potential of BCG to easily monitor cardiac deconditioning.