Abstract Background An assumption was made that results of programme evaluation lead to better understanding for whom this intervention may work. The aim of the article is to compare the changes in physical activity of the intervention programme participants depending on subjective assessment of its impact. Methods The data were obtained from 14- to15-year-old Polish girls (N = 1120) from 48 random selected secondary schools participating in the 1-year Healthy Me programme in the 2017/2018. Schools were randomly assigned to one of two types of intervention or to a control (null) group. Satisfaction with the programme according to 21 criteria was measured retrospectively just after the intervention. Change in MVPA (moderate-to-vigorous physical activity) during the programme implementation was assessed in relation to satisfaction level, and adjusted for initial MVPA. Results In total, the MVPA did not change significantly comparing pre- and post-intervention surveys (3.94 ± 1.94 vs. 3.87 ± 1.93)—P = 0.093. However, the perceived notable improvement of functioning in 10 out of 21 areas was related to the unquestionable increase in MVPA (P ≤ 0.001). With respect to the four impact areas, an interaction was demonstrated between an intervention group and an improvement in the domain-specific functioning. The beneficial impact of the programme on these areas was associated with the improvement of physical activity only in case of full and null intervention. Conclusions Indicators related to the implementation process and the results obtained during the Healthy Me programme evaluation could represent a change in motivational and environmental factors that indirectly affects adolescent girl’s physical activity.