Depression is highly prevalent among university students. Internet-based interventions have been found to be effective in addressing depressive symptoms, but it is open if this also applies to interventions directed at academic stress. It is also largely unclear if the techniques employed in such programs provide significant additional benefits when controlling for non-specific intervention effects. A sample of N = 200 students with elevated levels of depression (CES-D ≥ 16) of a large distance-learning university were randomly assigned to either an Internet- and App-based stress intervention group (IG; n = 100) or an active control group (CG; n = 100) receiving an Internet-based psychoeducational program of equal length. Self-report data was assessed at baseline, post-treatment (7 weeks) and three-month follow-up. The primary outcome was depression (CES-D) post-treatment. Secondary outcomes included mental health outcomes, modifiable risk factors, and academic outcomes. We found significant between-group effects on depressive symptom severity (d = 0.36; 95% CI: 0.08–0.64), as well as behavioral activation (d = 0.61; 95% CI: 0.30–0.91), perceived stress (d = 0.45; 95% CI: 0.18–0.73), anxiety (d = 0.35; 95% CI: 0.03–0.67) and other secondary outcomes post-treatment. Effects on depression were sustained at three-month follow-up. Response rates for depressive symptoms were significantly higher in the IG (26%) than the CG (14%) at post-test (χ²=4.5, p = 0.04), but not at three-month follow-up (p = 0.454). We also found significant effects on relevant academic outcomes, including work impairment (follow-up; d = 0.36), work output (post-treatment; d = 0.27) and work cutback (follow-up; d = 0.36). The intervention was more effective for depressive symptoms compared to the CG, and so controlling for unspecific intervention effects. This suggests that specific techniques of the intervention may provide significant additional benefits on depressive symptoms. Trial registration: German Clinical Trial Registration (DRKS): DRKS00011800 (https://www.drks.de/drks_web/navigate.do?navigationId=trial.HTML&TRIAL_ID=DRKS00011800).