Muscle atrophy and neuromuscular de-conditioning occur in response to space flight and bed-rest. In this study, we investigated the efficacy of flywheel training to conserve jumping power and height during 90 days bed rest. Twenty-four young healthy men underwent strict bed-rest (-6 degrees head down tilt) for 90 days. Eight participants were assigned to a flywheel group (FW) and 16 to a control group (Ctrl). The ground reaction force was measured during vertical jump tests twice during baseline data collection, and on day 4, 7, 14, 90 and 180 of recovery. In half of the participants, jump tests were also performed within minutes after re-ambulation and on four more occasions during the first 2 days of recovery. Jump height was reduced from 40.6 cm (SD 6.1 cm) during the first baseline measurement to 27.6 cm (SD 5.6 cm) on day 4 of recovery in Ctrl, but only from 38.6 cm (SD 3.9 cm) to 34.4 cm (SD 6.5 cm) in FW (P < 0.001). At the same time, peak power was reduced from 47.4 W/kg (SD 8.0 W/kg) to 34.5 W/kg in Ctrl, but only from 46.2 W/kg (6.0 W/kg) to 42.2 W/kg SD 4.6 W/kg) in FW (P < 0.001). Jump height and peak power were completely recovered after 163 and 140 days in Ctrl, respectively, and after 72 and 18 days in FW (regression analysis). In conclusion, flywheel exercise could effectively offset neuromuscular de-conditioning during bed-rest, and led to full recovery at an earlier stage. These findings nourish the hope that adequate training paradigms can fully sustain neuromuscular function under microgravity conditions.