The hippocampus forms a central modulator of the HPA-axis, impacting the regulation of stress on brain structure, function, and behavior. The current study assessed whether three different types of 3-months mental training modules geared towards nurturing a) attention-based mindfulness, b) socio-affective skills, or c) socio-cognitive abilities may impact hippocampal integrity by reducing stress. We evaluated mental training-induced changes in hippocampal subfield volume and intrinsic functional connectivity, based on resting-state fMRI connectivity analysis in a group of healthy adults (N=332). We then related these changes to changes in diurnal and chronic cortisol levels. We observed increases in bilateral cornu ammonis volume (CA1-3) following the 3-months compassion-based module targeting socio-affective skills (Affect module), as compared to socio-cognitive skills (Perspective module) or a waitlist cohort that did not undergo an intervention. Structural changes were paralleled by increases in functional connectivity of CA1-3 when fostering socio-affective as compared to socio-cognitive skills. Moreover, training-related changes in CA1-3 structure and function consistently correlated with reduction in cortisol output. In sum, we provide a link between socio-emotional behavioral intervention, CA1-3 structure and function, and cortisol reductions in healthy adults.