The interplay between biarticular and monoarticular muscles of the knee and hip joints during bipedal squats (SQ ) requires adequate central-nervous control mechanisms to enable smooth and dynamic movements. Here, we investigated motor control between M. vastus medialis (VM), M. vastus lateralis (VL), and M. rectus femoris (RF) in 12 healthy male recreational athletes during SQ with three load levels (50%, 62.5%, and 75% of 3-repetition maximum) following a standardized strength training protocol (3 sets of 10 repetitions). To quantify differences in motor control mechanisms in both time and frequency domains, we analyzed (1) muscle covariation via correlation analyses, as well as (2) common neural input via intermuscular coherence (IMC) between RF, VM, and VL. Our results revealed significantly higher gamma IMC between VM-VL compared with RF-VL and RF-VM for both legs. Correlation analyses demonstrated significantly higher correlation coefficients during ascent periods compared with descent periods across all analyzed muscle pairs. However, no load-dependent modulation of motor control could be observed. Our study provides novel evidence that motor control during SQ is characterized by differences in common input between biarticular and monoarticular muscles. Additionally, muscle activation patterns show higher similarity during ascent compared with descent periods. Future research should aim to validate and extend our observations as insights into the underlying control mechanisms offer the possibility for practical implications to optimize training concepts in elite sports and rehabilitation.