In this study, we aimed to evaluate the effects of two therapeutic methods: home-based exercise and manual therapy (MT) or supervised exercise on pain and functional status in individuals with chronic nonspecific low back pain. In total, 60 individuals with LBP were included in this randomized study. All participants were treated for 6 weeks in one of two groups: the manual therapy group or the exercise therapy group. In addition, all participants were asked to perform an exercise program at home independently. Levels of pain, spinal mobility, disability, and abdominal and back muscle endurance were measured before and after 6 weeks of intervention. Results: After MT, disability was reduced by 70% (F = 42.2; p < 0.00; ηp2 = 0.99) and pain was reduced by 78% (F = 4.9; p < 0.00; ηp2 = 0.51). After exercise therapy, disability and pain were reduced by 78% (F = 11.5; p < 0.00; ηp2 = 0.78) and 68% (F = 9.4; p < 0.00; ηp2 = 0.41), respectively. Muscle endurance and lumbar spine mobility values were significantly higher in both groups after 6 weeks of intervention (p < 0.00). After 12 MT interventions, lumbar spine mobility increased by 40% (F = 1.9; p < 0.00; ηp2 = 0.24) and after exercise therapy by 38% (F = 28.4; p < 0.00; ηp2 = 0.82). Abdominal muscle endurance improved by 29% (F = 24.2; p < 0.00; ηp2 = 0.79) after MT and by 34% (F = 57.6; p < 0.00; ηp2 = 0.67) after exercise therapy; back muscle endurance improved by 18% (F = 48.6; p < 0.00; ηp2 = 0.78) after MT and by 20% (F = 14.2; p < 0.00; ηp2 = 0.76) after exercise therapy. After 6 weeks of intervention, there was no statistically significant difference between the pain, disability, and spinal mobility groups (p > 0.05). However, differences between groups in kinesiophobia (p = 0.02), back (p < 0.02) and abdominal (p < 0.03) muscle endurance values were statistically significant. Following the home exercise program and manual therapy, or the home exercise program and supervised exercise, LBP and disability had clinically significant reductions and functional status showed improvement.