Background: the main objective of this study was to evaluate the test-retest reliability of two different functional electromechanical dynamometry (FEMD)-controlled squat training protocols. Methods: twenty-eight healthy young adults volunteered to participate in this study. They attended the laboratory on four different days and performed four sessions: two of three sets of 12 repetitions at 75% 1RM and two of three sets of 30 repetitions at 50% 1RM. The range of movement (ROM), mean dynamic strength (MDS), peak dynamic strength (PDS), mean velocity (MV), peak velocity (PV), mean potency (MP), peak potency (PP), work (W), and impulse (I) were recorded. To evaluate the reliability of FEMD, the intraclass correlation coefficient (ICC), standard error of measurement (SEM), and coefficient of variation (CV) were obtained. Results: reliability was very high for ROM (CV: 3.72%, ICC: 0.95), MDS (CV: 1.09%, ICC: 1.00), PDS (CV: 1.97%, ICC: 1.00), and W (CV: 4.69%, ICC: 1.00) conditions at 50% 1RM and for ROM (CV: 3.90%, ICC: 0.95), MDS (CV: 0.52, ICC: 1.00), PDS (CV: 1.49%, ICC: 0.98), and W (CV: 4.14%, ICC: 1.00) conditions at 75% 1RM and high for the rest of variables at 50 and 75% 1RM. Conclusions: this study demonstrates that FEMD is a reliable instrument to measure ROM, MDS, PDS, MV, PV, PV, MP, MP, W, and I during both squat protocols (50 and 75% 1RM) in healthy young adults.