Background: This study examines the relationship between adolescents' biophysiological stress (i.e. cortisol, alpha-amylase and oxidative stress) and the development of grit and school engagement over one school year. Aims: The study aims to identify how objective stress affects grit and three dimensions of school engagement. Based on the conservation of resources (COR) theory, the study considers lower- and higher-track school students and their genders. Sample: The sample consists of secondary school students (N = 82; M[subscript Age] = 13.71; SD = 0.67; 48% girls) from Germany. Methods: Students participated in a questionnaire and a biophysiological study in the first semester (t1) of the school year and completed the same questionnaire at the end of the school year (t2). After conducting whole-sample analysis, a multi-group cross-lagged panel model was calculated to identify differences among students at lower- and higher-track schools. Results: Whole-sample analysis reveals that students who exhibit high levels of cortisol report lower cognitive school engagement at t2, whereas students who exhibit high levels of alpha-amylase exhibit less grit at t2. Additionally, lower-track students who exhibited high cortisol levels reported lower cognitive and emotional school engagement throughout the school year. Furthermore, higher-track students with high oxidative stress levels reported lower grit and behavioural school engagement at t2. Conclusions: Examining the relationship between biophysiological stress markers and grit and school engagement of students at lower- and higher-track schools indicates that the educational context and its specific subculture shapes physiological stress reactions, which are related differently to grit and engagement dimensions.