Effective treatment for bipolar articular cartilage lesions in the knee remains a clinical challenge. Lower extremity malalignment is a risk factor for treatment failures, which can be addressed by tibial or femoral osteotomy. The purpose of this study was to compare outcomes among patients who underwent knee joint restoration by osteochondral allograft (OCA) transplantation with concurrent or staged realignment osteotomy. With Institutional Review Board approval, patients undergoing bipolar OCA transplantation with concurrent or staged distal femoral osteotomy (DFO) or high tibial osteotomy (HTO) were analyzed. Patients were categorized by osteotomy type (DFO and HTO) and timing (concurrent and staged). Patient-reported outcome measures (PROMs), revisions, failures, and complications were examined preoperatively (baseline), 3, 6, 12, and 24 months after OCA transplantation; change scores from preoperative values were used for analysis. A total of 23 patients met inclusion criteria (15 males); 13 (56.5%) received HTO (5 concurrent), while 10 (43.5%) received DFO (5 concurrent). There were no significant differences in complication rates between concurrent and staged osteotomies. Primary bipolar OCA transplantation with osteotomy was associated with successful outcomes in 70% of patients; four patients underwent revision (17.4%) and three (13.0%) failed and were treated by total knee arthroplasty. Further, the four patients undergoing revision met functional criteria for success at final follow-up, resulting in a 2-year functional survival rate of 87.4%. Aside from Patient-Reported Outcomes Measurement Information System (PROMIS) physical function, all PROMs for concurrent and staged osteotomies improved from baseline to 2 years postoperatively. Concurrent osteotomies of both types were associated with significantly lower pain scores at 12 months (p = 0.04), compared with staged osteotomies. Apart from Single Assessment Numerical Evaluation (SANE), more PROM improvement was observed for concurrent osteotomies at 2 years. Improvements in PROMs for patients undergoing OCA transplantation combined with osteotomy were observed at 2-year follow-up. PROMs for concurrent osteotomy were consistently greater than staged osteotomy, lending support to addressing lower extremity malalignment with bipolar OCA transplantation in the knee during a single surgery when possible.