The physical activity-related health competence (PAHCO) model assumes that individuals require movement competence, control competence, and self-regulation competence to lead a healthy, physically active lifestyle. Although previous research has already established some measurement factors (n = 8) of the three dimensions, no attempts have so far been made to statistically aggregate them on the sub-competence level. Therefore, the goal of the present study was to test two additional factors for PAHCO and subsequently model the second-order structure with two samples from the fields of rehabilitation and prevention. We conducted two questionnaire surveys with persons with multiple sclerosis (n = 475) and teaching students undergoing a basic qualification course in physical education (n = 502). After performing exploratory items analysis, we used second-order confirmatory factor analysis (CFA) and multidimensional scaling to investigate whether the scales could be bundled in accordance with the PAHCO model. The CFAs with 10 factors (42 items) demonstrated a good model fit. In contrast, the second-order analysis with a simple loading structure on the three sub-competencies revealed an unacceptable model fit. Instead, a second-order model variant was preferred [comparative fit index (CFI) = 0.926, root mean square error of approximation (RMSEA) = 0.048, standardized root mean square residual (SRMR) = 0.065] in which body awareness and self-efficacy had theory-conform cross-loadings. The results of multidimensional scaling (two-dimensional solution) were in line with the extracted second-order structure. The present results suggested that the extension of the measurement instrument to 10 first-order factors was psychometrically justified for the two populations. The results from the second-order analyses provided the basis for the creation of sum scores, representing manifest indicators of movement competence, control competence, and self-regulation competence. Future studies are needed that cross-validate the extended measurement model with other populations and that relate the sub-competencies of PAHCO to indicators of health-enhancing physical activity.