No studies have analysed the acute effects of the FIFA 11+ and Harmoknee warm-up programmes on major physical performance measures. The aim of this study was to analyse the acute (post-exercise) effects of the FIFA 11+, Harmoknee and dynamic warm-up routines on several physical performance measures in amateur football players. A randomized, crossover and counterbalanced study design was used to address the purpose of this study. A total of sixteen amateur football players completed the following protocols in a randomized order on separate days: a) FIFA 11+; b) Harmoknee; and c) dynamic warm-up (DWU). In each experimental session, 19 physical performance measures (joint range of motion, hamstring to quadriceps [H/Q] strength ratios, dynamic postural control, 10 and 20 m sprint times, jump height and reactive strength index) were assessed. Measures were compared via a magnitude-based inference analysis. The results of this study showed no main effects between paired comparisons (FIFA 11+ vs. DWU, Harmoknee vs. DWU and Harmoknee vs. FIFA 11+) for joint range of motions, dynamic postural control, H/Q ratios, jumping height and reactive strength index measures. However, significant main effects (likely effects with a probability of >75–99%) were found for 10 (1.7%) and 20 (2.4%) m sprint times, demonstrating that both the FIFA 11+ and Harmoknee resulted in slower sprint times in comparison with the DWU. Therefore, neither the FIFA 11+ nor the Harmoknee routines appear to be preferable to dynamic warm-up routines currently performed by most football players prior to training sessions and matches.