Although participation rates of women in science, technology, engineering, and mathematics (STEM) are continually improving, low rates are still an issue in many countries. While previous studies found positive effects of online mentoring for increasing girls’ interests in STEM, research concerning explanatory mechanisms is lacking. We found evidence that in a 1‐year online mentoring program for girls (age: M = 13.82 years, N = 998) in STEM, suitably implemented mentoring (operationalized via relationship quality in a program that systematically incorporates structural and organizational aspects of successful mentoring) was associated with positive changes in the learning environments of the mentees (as indicated by their increasing educational capital). These positive changes were associated with increases in the program‐related mentoring outcomes STEM activities and elective intentions in STEM. Finally, we found that suitably implemented online mentoring was indirectly related to an increase in these two mentoring outcomes via an increase in educational capital. These results indicate the importance of paying close attention to learning environments when planning interventions.