Purpose The ability of kinematic alignment (KA) to consistently restore trochlea anatomy in total knee arthroplasty (TKA) is unknown despite recreation of constitutional anatomy being its rationale for use. The purpose of this study was to assess if alignment choice in TKA effects the ability to restore the native trochlea groove. Methods One hundred and twenty-two consecutive patients undergoing robotic-assisted TKA using the MAKO image-based robotic platform had simulated femoral components placed according to kinematic, mechanical and functional alignment principals. Implant position and trochlea restoration between groups were compared. Restoration was assessed by shift (medial–lateral) and depth relative to the native groove from three consistent points; full extension (0°), mid-flexion (30°–40°) and deep flexion (70°–80°). Results Three hundred and sixty-six alignment options were analysed. Femoral alignment was significantly different between groups. Of KA, 13.1% compared to 3.3% of FA plans were outside safe coronal boundaries. The trochlear groove was translated the most by MA compared to KA and FA (full extension, MA 7.84 ± 1.99 mm lateral to the native groove, KA 6.40 ± 2.43 mm and FA 6.88 ± 1.74 mm, p  ≤ 0.001). In full extension, FA most closely restored the trochlear groove depth in all three positions of flexion. Conclusion Alignment philosophy led to significant differences in trochlea groove recreation. A kinematically placed femoral component led to positioning considered unsafe in over 13% of cases. A functionally placed femoral component most closely restored trochlea depth in all three positions of flexion.