The persistence of quadriceps weakness represents a major concern following anterior cruciate ligament reconstruction (ACLR). The underlying adaptations occurring in the activity of spinal motoneurons are still unexplored. This study examined the discharge patterns of large populations of motor units (MUs) in the vastus lateralis (VL) and vastus medialis muscles following ACLR. Nine ACLR individuals and 10 controls performed unilateral trapezoidal contractions of the knee extensor muscles at 35%, 50% and 70% of the maximal voluntary isometric force (MVIF). High‐density surface electromyography (HDsEMG) was used to record the myoelectrical activity of the vasti muscles in both limbs. HDsEMG signals were decomposed with a convolutive blind source separation method and MU properties were extracted and compared between sides and groups. The ACLR group showed a lower MVIF on the reconstructed side compared to the contralateral side (28.1%; P < 0.001). This force deficit was accompanied by reduced MU discharge rates (∼21%; P < 0.05), lower absolute MU recruitment and derecruitment thresholds (∼22% and ∼22.5%, respectively; P < 0.05) and lower input–output gain of motoneurons (27.3%; P = 0.009). Deficits in MU discharge rates of the VL and in absolute recruitment and derecruitment thresholds of both vasti MUs were associated with deficits in MVIF (P < 0.05). A strong between‐side correlation was found for MU discharge rates of the VL of ACLR individuals (P < 0.01). There were no significant between‐group differences (P > 0.05). These results indicate that mid‐ to long‐term strength deficits following ACLR may be attributable to a reduced neural drive to vasti muscles, with potential changes in excitatory and inhibitory synaptic inputs. Key points Impaired expression and control of knee extension forces is common after anterior cruciate ligament reconstruction and is related to high risk of a second injury. To provide novel insights into the neural basis of this impairment, the discharge patterns of motor units in the vastus lateralis and vastus medialis were investigated during voluntary force contractions. There was lower knee extensor strength on the reconstructed side with respect to the contralateral side, which was explained by deficits in motor unit discharge rate and an altered motoneuronal input–output gain. Insufficient excitatory inputs to motoneurons and increased inhibitory afferent signals potentially contributed to these alterations. These results further our understanding of the neural underpinnings of quadriceps weakness following anterior cruciate ligament reconstruction and can help to develop effective rehabilitation protocols to regain muscle strength and reduce the risk of a second injury. figure legend Changes in activity of motor units underlying deficits in knee extension strength following anterior cruciate ligament reconstruction (ACLR). The behaviour of motor units was assessed by decomposing high‐density surface electromyographic signals that were recorded from the vasti muscles of ACLR and control soccer players during submaximal trapezoidal contractions. The lower knee extension strength of the reconstructed side with respect to the contralateral side was explained by deficits in motor unit recruitment and derecruitment thresholds, by deficits in motor unit discharge rate of the vastus lateralis and by an altered input–output gain of motoneurons. Synaptic alterations and changes at muscle unit level potentially contributed to changes in motor unit activity. Correction made on 15 November 2021, after first online publication: The two preceding sentences have been updated to provide greater clarity.