Background Increased knee flexion is required for deep squatting in the daily life of the non-western population as well as in many sports activities. The purpose of this study was to estimate as well as to compare knee joint contact forces during heel contact (HC) and heel rise (HR) deep squatting in 10 healthy young Indian participants. Materials and Methods Kinematic data were captured using a 12-camera Motion Analysis system. Kinetic data were collected using two Kistler force plates. EMG of 6 lower limb muscles was monitored by Noraxon wireless EMG. OpenSim musculoskeletal model was customized to increase the maximum knee flexion capability of the existing model and knee joint contact forces were estimated. Results A significant difference in tibiofemoral (p < 0.001) as well as patellofemoral (p = 0.006) knee joint contact force (KJCF) was observed between HC and HR squatting. The resultant maximum tibiofemoral KJCF was 5.9 (± 0.54) times body weight (BW) and 5.3 (± 0.6) BW for the HC and HR, respectively. The resultant maximum patellofemoral KJCF was 7.8 (± 0.57) BW and 7.1 (± 0.73) BW for the HC and HR, respectively. Conclusion The findings can provide implications for physiotherapists to design rehabilitation exercise protocols, exercise professionals, and the development of high flexion knee implants.