Navigation-based total knee arthroplasty (TKA) has proven its value for restoration of the limb axis. However, patient-orientated results after TKA show a wide variation from the correct implantation technique. Nonphysiological kinematics without posterior femoral rollback and tibial internal rotation in flexion could be one reason for this. We postulated that a modified gap-balancing technique with navigation of the tibia alone, in comparison to a conventional navigated technique, would: (1) obtain lateral femoral rollback, (2) alter condylar liftoff without midflexion instability, (3) significantly differ in femoral and tibial cuts, (4) not be inferior in leg-axis restoration and (5) be comparable in clinical short-term scores. In this prospective study, we compared in vivo navigation-based kinematics pre- and postoperatively of 40 consecutive TKA comprising 21 conventional navigation-based TKA and 19 TKA with the modified gap-balancing technique and a reduced navigation workflow. All cuts were double checked and compared with cuts proposed by the navigation system. Clinical results were assessed preoperatively and six months postoperatively. The modified gap-balancing technique resulted in significantly increased lateral femoral rollback (mean 16.3 mm) and lateral condylar liftoff (mean 1.3 mm) compared to the conventional group. The modified technique comprised an average of 2.1 mm less distal femoral resection and an average of 4° less external rotation and 3.5° more flexion of the femoral component compared with the control group. Average tibial resection height was 1.1 mm greater and average tibial slope was 0.5° elevated compared to the control group. A neutral leg axis was achieved in all cases. Results showed no significant differences in clinical scores between groups. A partial navigation solely of the tibial cut can securely restore the leg axis. Modification of the surgical technique can possibly reproduce more physiological knee kinematics with higher lateral femoral rollback in flexion without midflexion instability. This might help reduce postoperative problems with the new implant and thus reduce the amount of unsatisfactory results. Despite equal short-term results, mid- to long-term results are needed to prove whether or not this correlates with better clinical results and at least equal implant longevity.