Background: Low physical performance is a predictor of morbidity and mortality. This study looks at long-term effects of an exercise intervention on maximal step-up height (MSH) in individuals with low physical function. Factors associated with changes in MSH was studied. Methods: Female patients (n = 101), mean (SD) age of 52 (11) years, were recruited for a 3-month group exercise intervention including 2-3 sessions/week of mixed aerobic fitness and strength training. MSH, weight, body mass index (BMI), waist circumference, maximal oxygen consumption (VO 2-max), self-reported health (SF-36) and physical activity (PA) were measured at baseline (T0), after 3 months (T1) and after 14-30 (mean 22) months (T2). Relationships between changes in MSH (cm) and age, baseline MSH, time to follow-up, changes in anthropometric measurements, VO 2-max, SF-36 and PA were studied with regression analyses. Results: MSH, significantly, increased from T0 to T1, 27.2 (5.7) to 29.0 (5.5) cm and decreased to 25.2 (5.5) cm at T2. Time to follow-up (B = − 0.42, p < 0.001) and change in BMI (B = − 0.29, p = 0.012) correlated significantly to changes in MSH. Waist circumference, VO 2-max, PF and exercise/physical activity levels were significantly improved at T2, while BMI did not change. In a univariate logistic regression model, maintenance of MSH correlated to the extent of mixed training (OR 3.33, 95% CI 1.25-8.89). In a multivariate logistic regression model adjusted for important factors the correlation was not significant. However, MSH was significantly higher in individuals participating in 2-3 session per week compared to one session. Conclusions: A 3-month group exercise intervention increased MSH, improved fitness, decreased risk in female patients with elevated cardio-metabolic risk. After an average of 22 months MSH was reduced while positive effects remained for waist circumference, VO 2-max, physical function and physical activity. However, regular group exercise 2-3 times per week with mixed aerobic fitness and strength training was associated with maintenance of MSH in a subgroup of patients. We suggest that such an intervention including regular support from healthcare professionals is a successful approach for maintaining improved leg-muscle strength among primary care patients.