Purpose <p>The increasing demands of both training and competition have heightened the need for load monitoring among soccer players. However, adopting metrics that comprehensively capture the intricacies of neuromuscular fatigue remains a&#xa0;challenge. Assessing low-frequency fatigue may contribute to filling this gap, as it provides an objective measure to evaluate muscle function readiness. The aim of this study was to examine whether variability in low-frequency fatigue morning scores is related to acute changes in external training load throughout the in-season microcycle.</p> Methods <p>In total, 18 young elite soccer players (age: 17.56 ± 0.68&#xa0;years; height: 179.33 ± 7.71 cm; weight: 70.78 ± 7.20 kg) participated in this study. Low-frequency fatigue was assessed using a&#xa0;specialized device that records the evoked forces of the knee extensor muscles in response to submaximal electrical stimulation at both low and high frequencies. This evaluation was carried out every morning throughout the microcycle, before training and competition, and the outcome was analyzed in relation to the previous day’s external training load.</p> Results <p>Reduced linear mixed-effects regression models showed that low-frequency fatigue morning scores were associated with the previous day’s training total running distance, high-speed running distance, number of high-intensity accelerations and decelerations, and Player Load (<i>R</i>² = 0.32–0.34).</p> Conclusion <p>These results suggest that morning low-frequency measurements might be sensitive to acute changes in external training load throughout an in-season soccer microcycle. Specifically, managing total running distance and the number of high-intensity accelerations during the training session may contribute to alleviating the decline in muscle function on the following day.</p>