Background: Anterior cruciate ligament (ACL) injuries induce neurophysiological alterations that may persist after rehabilitation, affecting motor control and neuromuscular coordination. This study aimed to examine residual neuromuscular deficits in team-sport athletes who had undergone ACL reconstruction by assessing phase-specific force production, electromyographic (EMG) signal complexity, and inter-limb asymmetries. Methods: Thirteen competitive team-sport athletes (men: n = 5, 24.2 ± 2.9 years; women: n = 8, 21.5 ± 1.9 years) participated in this cross-sectional study. Force production and surface EMG activity of the vastus lateralis (VL) and biceps femoris (BF) were recorded during an iso-inertial squat. Force data were analyzed globally and according to the concentric (CON) and eccentric (ECC) phases. Inter-limb asymmetries were calculated, and linear analyses were applied to force and EMG variables, while EMG complexity was assessed using sample entropy (SampEn). Results: Significant inter-limb differences were observed during the ECC phase, with lower peak and mean force values in the ACL-reconstructed limb (ACLR; p < 0.05), whereas no statistically significant inter-limb differences were identified in the global or CON analyses. Conventional EMG measures showed no statistically significant inter-limb differences. VL SampEn values were descriptively lower in the ACLR than in the contralateral non-reconstructed limb (ACLN), but this difference did not reach statistical significance (p = 0.063; Hedges’ g = −0.67). Inter-limb asymmetries showed substantial inter-individual variability, particularly across movement phases. Athletes following ACL reconstruction exhibited residual deficits in eccentric force production, whereas conventional EMG activation did not differ significantly between limbs. Phase-specific force analysis may therefore identify residual ECC deficits that are not apparent in global or concentric analyses. Although nonlinear EMG metrics may provide complementary information on neuromuscular organization beyond that captured by conventional amplitude-based measures, the present SampEn findings should be considered exploratory and hypothesis-generating rather than evidence of a confirmed alteration in neuromuscular complexity. Larger, adequately powered studies incorporating robustness and sensitivity analyses are required to determine the relevance of entropy-based EMG measures following ACL reconstruction.