Early life maltreatment (ELM) has severe and lasting effects on the individual, which might also impact the next generation. On an endocrine level, the hypothalamus–pituitary–adrenal axis has been suggested to play an important role in the interplay between ELM and the development of mental disorders. Several studies have revealed that maternal post-awakening cortisol concentration, maternal sensitivity, maternal ELM and psychopathology are associated with children's cortisol levels. We investigated the post-awakening cortisol concentrations in 6- to 11-year-old children (N = 53) whose mothers either had experienced ELM and had developed a lifetime mental disorder (N = 15 ELM and disorder group), had experienced ELM without developing a mental disorder (N = 12 ELM-only group), or had neither experienced ELM nor developed a mental disorder (N = 26 HC-group). Furthermore, we assessed maternal post-awakening cortisol concentrations, maternal psychopathology, and sensitivity. Multilevel analysis revealed higher cortisol at awakening (S1) levels in children of mothers with ELM and disorder. Maternal cortisol at awakening (S1) also predicted the child's cortisol at awakening (S1), and no effect of maternal sensitivity could be found. The current results replicate an attunement of cortisol levels (S1) between mothers and children and suggest an association between the children's endocrine stress system and maternal factors such as ELM and psychopathology.