Noncommunicable diseases (NCDs) and their underlying risk factors are seen as major public health problems that threaten health and welfare systems worldwide. The holistic and resource oriented Health Promoting School (HPS) approach can serve as an appropriate framework for the prevention and control of NCDs. The paper aimed to map the implementation of HPS activities in German schools and to examine associations with potential influencing factors. A series of cross-sectional online studies including five federal states and 5006 school principals (40.2% males, 50.8% females) from primary and secondary public schools was conducted from 2013 to 2018. Principal component analysis (PCA) resulted in two factors of HPS implementation (F1: concrete HPS action, F2: capacity building for HPS). Comparing both factors, a lower implementation level could be identified for HPS capacity building with lowest mean values found for regular teacher training and intersectoral collaboration. Multiple binary regression analyses revealed significant associations between low HPS implementation and male gender (OR: 1.36 to 1.42), younger age (OR: 1.47 to 1.90), secondary school (OR: 1.78 to 3.13) and federal state (Lower Saxony = OR: 1.27 to 1.45; Schleswig-Holstein = OR: 1.95 to 2.46). Moreover, low access to resources, decision-latitude and perceived educational benefits were independently associated with both factors of HPS implementation. Based on the results of this study, there is a need to support schools in their capacity building for health (e.g., regular teacher training, cooperation with local health services). Moreover, considering the core mission of schools, more evidence of the educational impact of health promotion and its translation into the language of education is needed for secondary schools in particular.