ABSTRACT To assess the effect of active and passive intra-interval recovery modes in time-efficient high-intensity interval training (HIT) on cardiorespiratory fitness, autonomic function, and endothelial function in sedentary middle-aged men. Participants (n = 62; age: 49.5 ± 5.8 y; BMI: 29.7 ± 3.7 kg·m−2) completed the assessments of cardiorespiratory fitness, flow-mediated dilation (FMD) and heart rate variability before being randomly allocated to control (CON; n = 14), moderate intensity continuous training (MICT; n = 15), HIT with passive (P-HIT; n-15), or active recovery (A-HIT; n = 15). Participants performed thrice weekly exercise sessions for 12 weeks. MICT completed 50–60 min of continuous cycling at 60–70% heart rate (HR) maximum. HIT completed 30-s work intervals (∼85% HR) interspaced with 2.5 min of active or passive recovery. All exercise modalities increased oxygen uptake (V̇O2) (MD: ≥ 3.1 ml·kg−1·min−1, 95%CI: 1.5–4.7 ml·kg−1·min−1; P < 0.001), power output (MD: ≥ 26 W, 95%CI: 15–37 W; P < 0.001) and cycle duration (MD: ≥ 62 s, 95%CI: 36–88 s; P < 0.001) at 85% HRM. Significant pre-to-post differences were observed among all exercise groups for FMD (MD: ≥ 3.4%, 95%CI: 0.3–6.5%; P < 0.05), while MICT and P-HIT significantly increased the standard deviation of all NN intervals (SDNN) pre-to-post intervention (MD: ≥ 7 ms, 2–13 ms; P ≤ 0.05). Time-efficient HIT elicits significant improvements in cardiorespiratory fitness, FMD and autonomic modulation following a thrice weekly 12-week exercise intervention among sedentary middle-aged men. Active recovery between successive high-intensity intervals provided no additional benefit among this deconditioned cohort.