Aims: To evaluate the effectiveness of a dual approach involving time-restricted eating (TRE) at different times of the day combined with physical activity (PA) on functional capacity and metabolic health in overweight or obese women. Methods: Random allocation of sixty-one participants into four groups: early time-restricted eating plus physical activity (ETRE-PA, n = 15, 31.8 ± 10.76 years, 89.68 ± 13.40 kg, 33.5 ± 5.53 kg/m2), late time-restricted eating with physical activity (LTRE-PA, n = 15, 30.60 ± 7.94 years, 94.45 ± 15.36 kg, 34.37 ± 7.09 kg/m2), late time-restricted eating only (LTRE, n = 15, 27.93 ± 9.79 years, 88.32 ± 10.36 kg, 32.71 ± 5.15 kg/m2) and a control group (CG, n = 15, 36.25 ± 11.52 years, 89.01 ± 11.68 kg, 33.66 ± 6.18 kg/m2). The intervention lasted for 12 weeks in all groups. Both the ETRE-PA and LTRE-PA groups engaged in a rigorous combined aerobic and resistance-training program. Results: Significant reductions in body weight and body mass index were observed in the ETRE-PA and LTRE-PA groups compared to the CG and LTRE groups post-intervention (p < 0.0005). Only the ETRE-PA group exhibited a significant decrease in fat mass (p = 0.02), low-density lipoprotein cholesterol (p = 0.01), and aspartate aminotransferase (p = 0.002). Significant reductions in alanine aminotransferase levels were observed in the ETRE-PA (p = 0.004) and LTRE-PA (p = 0.02) groups. These two latter groups achieved higher performances in the 6-min walking test, bench press, 30-s squat, crunch test, vertical jump (p < 0.0005 for both), and leg extension (p < 0.02 for both) when compared to the LTRE and CG groups. Conclusion: The integration of TRE with PA leads to greater improvements in body composition, lipid profile, and physical performance, with no significant differences between the ETRE-PA and LTRE-PA approaches. This combined strategy offers a promising solution for overweight and obese women.