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A large body of literature has shown the effectiveness of mindfulness‐based interventions (MBI) on stress‐reduction. However, little is known about their effects on psychobiological stress‐markers in daily life through an ecological momentary assessment approach. Our study examines the effects of MBI on state mindfulness, perceived stress, and indicators of sympathetic‐nervous‐system (saliva alpha‐amylase, sAA) and hypothalamic‐pituitary‐adrenal‐axis (saliva cortisol, sCort) activation in daily life. Twenty‐eight individuals participated in a three‐month MBI (IG) and were compared to 46 controls (CG). An ecological momentary assessment (EMA) was used to assess mindfulness, stress, sAA and sCort at six measurements per day on two days each before and after the MBI. Multilevel‐modeling was used to analyze the data on a moment‐to‐moment and averaged day‐level. The IG showed decreased sAA levels …