Aims The aim of this study was to compare robotic arm-assisted bi-unicompartmental knee arthroplasty (bi-UKA) with conventional mechanically aligned total knee arthroplasty (TKA) in order to determine the changes in the anatomy of the knee and alignment of the lower limb following surgery. Methods An analysis of 38 patients who underwent TKA and 32 who underwent bi-UKA was performed as a secondary study from a prospective, single-centre, randomized controlled trial. CT imaging was used to measure coronal, sagittal, and axial alignment of the knee preoperatively and at three months postoperatively to determine changes in anatomy that had occurred as a result of the surgery. The hip-knee-ankle angle (HKAA) was also measured to identify any differences between the two groups. Results The pre- to postoperative changes in joint anatomy were significantly less in patients undergoing bi-UKA in all three planes in both the femur and tibia, except for femoral sagittal component orientation in which there was no difference. Overall, for the six parameters of alignment (three femoral and three tibial), 47% of bi-UKAs and 24% TKAs had a change of < 2° (p = 0.045). The change in HKAA towards neutral in varus and valgus knees was significantly less in patients undergoing bi-UKA compared with those undergoing TKA (p < 0.001). Alignment was neutral in those undergoing TKA (mean 179.5° (SD 3.2°)) while those undergoing bi-UKA had mild residual varus or valgus alignment (mean 177.8° (SD 3.4°)) (p < 0.001). Conclusion Robotic-assisted, cruciate-sparing bi-UKA maintains the natural anatomy of the knee in the coronal, sagittal, and axial planes better, and may therefore preserve normal joint kinematics, compared with a mechanically aligned TKA. This includes preservation of coronal joint line obliquity. HKAA alignment was corrected towards neutral significantly less in patients undergoing bi-UKA, which may represent restoration of the pre-disease constitutional alignment (p < 0.001). Cite this article: Bone Joint J 2020;102-B(11):1511–1518.