Post-activation performance enhancement (PAPE) is an acute performance increase in voluntary exercises induced by a conditioning activity. Due to the scarcity of evidence about the effectiveness of distinct protocols, the aim of this study was to compare the effects of two different flywheel PAPE protocols (half-squat and lunge exercises) on vertical and horizontal jump performance, as well as change-of-direction ability in female amateur footballers (n = 21). Each protocol consisted of 3 sets of 6 repetitions for the half-squat protocol or 10 repetitions for the lunge protocol, with two minutes of passive rest, performed with a conical pulley. Both protocols were followed by rests of two, eight, and twelve minutes for repeated countermovement jump (CMJ), triple hop, and change-of-direction test (modified T-505) testing. The fixed-effect model 2-ways-repeated measures ANOVA showed that there was no significant interaction between time and exercises performed (p > 0.05). There was no significant relationship between exercise specificity and performance in sport-specific tasks. Our results suggest that, within this population, neither flywheel protocol provided measurable PAPE benefits across varied time windows. The findings underscore the importance of strength levels in achieving PAPE benefits and question the specificity of PAPE protocols to targeted sport performance outcomes.