This study investigated the effect of home-based shallow and deep squat trainings on knee extension peak torque, muscle thickness, one-repetition maximum (1RM) leg press, and physical function in older individuals. Sixteen participants were randomly assigned to the shallow squat group (SS group; age, 71.0 ± 4.0 years) or deep squat group (DS group, age; 68.6 ± 3.6 years). Chairs of 40-cm height and chairs with a cushion of 20-cm height (60-cm in total) were used as the depth targets for squats, with participants instructed to sink until their hip touched the chair and cushion. Participants performed four sets of squats per day (35 repetitions per set), three days per week, for 12 weeks at their home. Knee extension peak torque, muscle thickness of quadriceps femoris (e.g., vastus lateralis, rectus femoris, and vastus intermedius), and physical function were measured at weeks 0 (baseline), 4, 8, and 12. Maximal isometric knee extension peak torque, muscle thickness, and walking speed did not change significantly over the 12-week training period in either group (P > 0.05). However, compared with the baseline, there was significant improvement in the results of 30-s sit-to-stand repetition tests after weeks 8 and 12 in both groups (P < 0.05). Additionally, 1RM leg press results were significantly improved after weeks 4 and 12 in the DS group, and weeks 4, 8, and 12 in the SS group (P < 0.05). Results indicate that home-based weight-bearing squat training improves lower limb function in older adults, as well as performance in physical functional tests related to activities of daily living. Moreover, such training benefits older adults regardless of whether squats are shallow or deep.