Considering the bilateral deficit, the sum of forces produced by each limb in a unilateral condition is generally greater than that produced by them in a bilateral condition. Therefore, it can be speculated that performing unilateral strength exercises may allow greater training workloads and subsequently greater neuromuscular adaptations when compared with bilateral training. Hence, the purpose of this study was to compare neuromuscular adaptations with unilateral vs. bilateral training in the knee extensor muscles. Forty-three recreationally active young women were allocated to a control, unilateral (UG) or bilateral (BG) training group, which performed 2 times strength training sessions a week for 12 weeks. Knee extension one repetition maximum (1RM), maximal isometric strength, muscle electrical activity, and muscle thickness were obtained before and after the study period. Muscle strength was measured in unilateral (right + left) and bilateral tests. Both UG and BG increased similarly their unilateral 1RM (33.3 ± 14.3% vs. 24.6 ± 11.9%, respectively), bilateral 1RM (20.3 ± 6.8% vs. 28.5 ± 12.3%, respectively), and isometric strength (14.7 ± 11.3% vs. 13.1 ± 12.5%, respectively). The UG demonstrated greater unilateral isometric strength increase than the BG (21.4 ± 10.5% vs. 10.3 ± 11.1%, respectively) and only the UG increased muscle electrical activity. Muscle thickness increased similarly for both training groups. Neither group exhibited pretesting 1RM bilateral deficit values, but at post-testing, UG showed a significant bilateral deficit (-6.5 ± 7.8%) whereas BG showed a significant bilateral facilitation (5.9 ± 9.0%). Thus, performing unilateral or bilateral exercises was not a decisive factor for improving morphological adaptations and bilateral muscle strength in untrained women. Unilateral training, however, potentiate unilateral specific strength gains.