Mobile app-based meditation is an effective self-care solution for depression, but limited evidence exists for the long-term benefits among autistic adults, who are at increased risk of experiencing depression. The primary goal of this study was to examine the feasibility and effectiveness of incorporating habit training into an app-based meditation intervention to maintain reductions in depressive symptoms among autistic adults. Participants were randomized to an App Only (who only received access to the meditation app), App + Habit Training (who received the meditation app and instructions for anchoring their app-based meditation to an existing routine), or a waitlist control group. All participants completed questionnaires at baseline, post-intervention, and 6 months post-intervention, and responded to SMS ecological momentary assessments regarding their meditation practice during the 8-week intervention and an 8-week follow-up period. The results show that the App + Habit Training group reported significantly more days with meditation per week during and after the intervention (p < 0.05) and also experienced a larger decrease in depression symptoms post-intervention and 6 months later (p < 0.05) relative to the control group. These findings demonstrate that app-based meditation habits are an effective self-care solution for autistic adults with depression, and anchoring is a promising strategy for establishing other healthy habits among autistic adults.