Few studies have compared the longer-term effects of physical activity interventions. Here we compare a 6-month physiotherapist-led, home-based physical activity program to a community group exercise program over 2 years. Healthy, sedentary community-dwelling 50–65 year olds were recruited to a non-randomised community group exercise program (G, n = 93) or a physiotherapist-led, home-based physical activity program (HB, n = 65). Outcomes included ‘sufficient’ physical activity (Active Australia Survey), minutes of moderate-vigorous physical activity (ActiGraph GT1M), aerobic capacity (2-min step-test), quality of life (SF-12v2), blood pressure, waist circumference, waist-to-hip ratio and body mass index. Outcome measures were collected at baseline, 6, 12, 18 and 24 months. Using intention-to-treat analysis, both interventions resulted in significant and sustainable increases in the number of participants achieving ‘sufficient’ physical activity (HB 22 v. 41%, G 22 v. 47%, P ≤ 0.001) and decreases in waist circumference (HB 90 v. 89 cm, G 93 v. 91 cm, P < 0.001) over 2 years. The home-based program was less costly (HB A$47 v. G $84 per participant) but less effective in achieving the benefits at 2 years. The physiotherapist-led, home-based physical activity program may be a low-cost alternative to increase physical activity levels for those not interested in, or unable to attend, a group exercise program. This study has been registered with the Australian New Zealand Clinical Trials Registry (ANZCTR), Clinical Trial Registration number ACTRN12611000890932.