To analyse the effects of four full squat (SQ) training programmes with different velocity loss (VL) thresholds (0%, 10%, 20%, and 40%) with blood flow restriction (BFR) implementation on muscle size, lower limb strength, and neuromuscular adaptations. Forty-six strength-trained men carried out an 8-week (16 sessions) SQ training programme with BFR that differed in the VL attained within the set: BFR 0% VL (BFR0, n = 11), BFR 10% VL (BFR10, n = 11), BFR 20% VL (BFR20, n = 11), and BFR 40% VL (BFR40, n = 13). The same inter-set recovery (2 minutes), sets (3), intensity (from 55% to 70% 1RM), and level of BFR (50% of arterial occlusion pressure) were established for all groups. Before and after the training intervention, the following tests were carried out: 1) vastus lateralis muscle size; 2) countermovement jump; 3) maximal isometric SQ test; 4) progressive loading SQ test; and 5) fatigue SQ test. Muscle hypertrophy increased as the VL increased (“group×time” interaction: p = 0.013). Only BFR20 significantly improved force production at various time intervals (“group×time” interactions: p ≤ 0.05). Moreover, effect sizes suggest that low-to-moderate VL thresholds maximize the improvements in SQ strength against different loads (BFR0: 0.47 1.75; BFR10: 0.61–1.96; BFR20: 0.71–2.18; BFR40: 0.38–1.53). In BFR contexts, low-to moderate VL thresholds should be prescribed to optimize leg strength performance. Extremely low VL (i.e., 0%) seemed insufficient to maximize strength gains, while higher VL thresholds are more effective for promoting muscle hypertrophy but may somewhat compromise strength improvements.