Besides having an unhealthy lifestyle contributing to premature mortality, inpatients with severe mental illness (SMI) use high dosages of medication. Previous research has shown improved health after lifestyle improvements in SMI. In addition, we aimed to retrospectively study whether a multidisciplinary lifestyle enhancing treatment (MULTI) was associated with changes in medication use after 18 months, as compared with patients that continued treatment as usual (TAU) and explored mediation by a change in physical activity. We conducted an observational study within a cohort of inpatients with SMI, who received MULTI (N = 65) or continued TAU (N = 49). Data on their somatic and psychotropic medications were collected, converted into defined daily dose (DDD), and analyzed using linear multilevel regression, correcting for baseline value and differences between groups in age, diagnosis, and illness severity. Compared with TAU, the DDD for psychotropic medication significantly decreased with MULTI (B = −0.55, P = 0.02). Changes in total activity did not mediate this association, suggesting that multiple components of MULTI contributed. Corrected between-group analyses for subgroups of medication were not possible due to lack of power and skewed distributions. Within-group data showed a decreased proportion of users as well as median DDD in both groups for almost all medications. In addition to previously reported health improvements after 18 months of MULTI, we observed a significant decrease in dose of psychotropic medication in MULTI compared to TAU. This first study evaluating a wide range of medications indicates a possible effect of lifestyle improvements on medication use in inpatients with SMI. Findings need to be confirmed in future controlled studies, however.