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There is not enough evidence on the impact of different speed endurance training regimes on footballers' ability to perform multiple shuttle run performance. This study examined the effect of 4 weeks of speed endurance maintenance (SEM) and speed endurance production (SEP) training on the 5-meter multiple shuttle run test (5-m MST) performance in young elite soccer players. A parallel two-groups, longitudinal design was used. Fifteen players were divided to either SEM (8 repetitions of 20-s all-out sprint interspersed with 40 s of recovery) or SEP (8 repetitions of 20-s all-out bout interspersed with 120 s of recovery) training group. SEM improved the ability to tolerate fatigue and maintained the performance development during the 5-m MST while SEP increased only the 1 st sprint showing, simultaneously, an increased fatigue index and performance decrement. The selection of which training regimes to prioritize should be based on the players' characteristics and individual game requirements Abbreviations: SEP: Speed Endurance Production; SEM: Speed Endurance Maintenance; PRE: Baseline; POST: End of experimental protocol; 5-m MST: 5-meters Multiple Shuttle Run Test; TD: Total Distance; FI: Fatigue Index; MSTdec: Percentage Decrement Score; BMI: Body Mass Index.