Optimising countermeasures for musculoskeletal deterioration during spaceflight is a priority for space agencies. We examined the impact of adding whey protein supplementation to resistive vibration exercise (RVE) on lumbar deconditioning during prolonged bed-rest. Participants (n=12) were enrolled in a cross-over design 21d bed-rest with RVE (2d/wk, 2-4min/session time-under-tension), whey protein supplementation plus RVE (NeX) and no-intervention control (CNT). Following bed-rest, NeX (‑2.2[7.0]%, P=0.370), but not RVE (‑5.6[6.4]%, P=0.0027), reduced paraspinal muscle atrophy compared to CNT (-6.1[5.5]%, P=0.00035). After 3d bed-rest, whole intervertebral disc (IVD) T2 increased in all groups (CNT: +5.3(2.5)%, P<0.0001; NeX: +6.3(1.8)%, P<0.0001; RVE: +6.3(1.9)%, P<0.0001) and remained at this level on day-21 of bed-rest (CNT: 5.5(2.6)%, P<0.0001; NeX: 6.0(1.8)%, P<0.0001; RVE: 6.2(2.8)%, P<0.0001). Increases in IVD T2 were greatest in the nucleus (10.9[1.1]%, P<0.0001), with reductions of T2 observed in the anterior annulus (‑4.4[1.0]%, P=0.00001) and increases in the posterior annulus (2.1[0.8]%, P=0.011). At 6d and 28d post‑bed-rest, IVD T2 was similar compared to baseline for all groups. A similar pattern was seen for IVD height, although a -3.8(4.6)% (P=0.0052) reduction of IVD height was seen 28d after bed-rest in the CNT group. The countermeasures did not impact on the presence or intensity of back pain during or after bed-rest. Participants reporting back pain on day-3 of bed‑rest had greater (P=0.013) increases in intervertebral disc volume than participants who did not. Whilst neither countermeasure impacted on IVD changes or back pain in prolonged bed-rest, NeX, but not RVE alone, ameliorated paraspinal muscle atrophy.