Background: Community-based recovery-oriented mental health services for people with severe mental disorders have not been fully implemented in Bulgaria, Croatia, Macedonia, Montenegro, and Romania. The RECOVER-E project facilitates the implementation of specialized mental health care delivered by setting up services, implementing the services, and evaluating multidisciplinary community mental health teams. The outcomes of the RECOVER-E project are assessed in a trial-based outcome evaluation in each of the participating countries with a health-economic evaluation linked to these trials. Objective: The aim of this protocol paper is to describe the methodology that will be used for the health-economic evaluation alongside the trials. Methods: Implementation sites have been selected in each of the five countries where hospital-based mental health services are available (care as usual [CAU]) for patients with severe mental disorders (severe depression, bipolar disorder, schizophrenia, and other psychotic disorders). The newly implemented health care system will involve community-based recovery-oriented mental health care (CMHC). At each site, 180 consenting patients will be randomized to either CAU or CMHC. Patient-level outcomes are personal and social functioning and quality-adjusted life years (QALYs). Data on participants' health care use will be collected and corresponding health care costs will be computed. This enables evaluation of health care costs of CMHC as compared with CAU, and these costs can be related to patient-level outcomes (functioning and QALY gains) in health-economic evaluation. Results: Data collection was started in December 2018 (Croatia), February 2019 (Montenegro), April 2019 (Romania), June 2019 (North Macedonia), and October 2019 (Bulgaria). The findings of the outcome evaluations will be reported for each of the five countries separately, and the five trials will be pooled for multilevel analysis on a combined dataset. Conclusions: The results of the health-economic evaluation of the RECOVER-E project will contribute to the growing evidence base on the health and economic benefits of recovery-oriented and community-based service models for health systems in transition.