Background: People living with HIV (PLWH) with a substance use disorder (SUD) tend to receive inadequate medical care in part because of a siloed healthcare system in which HIV and substance use services are delivered separately. Ideal treatment requires an interdisciplinary, team-based coordinated care approach, but many structural and systemic barriers impede the integration of HIV and SUD services. The current protocol describes the development and preliminary evaluation of a care coordination intervention (CCI), consisting of a tablet-based mobile platform for HIV and SUD treatment providers, an interagency communication protocol, and a training protocol. We hypothesize that HIV and SUD treatment providers will find the CCI to be acceptable, and that after receipt of the CCI, providers will: exhibit higher retention in dual care among patients, report increased frequency and quality of communication, and report increased rates of relational coordination. Methods/design: A three phase approach is used to refine and evaluate the CCI. Phase 1 consists of in-depth qualitative interviews with 8 key stakeholders as well as clinical audits of participating HIV and SUD treatment agencies. Phase 2 contains functionality testing of the mobile platform with frontline HIV and SUD treatment providers, followed by refinement of the CCI. Phase 3 consists of a pre-, post-test trial with 30 SUD and 30 HIV treatment providers. Data will be collected at the provider, organization, and patient levels. Providers will complete assessments at baseline, immediately post-training, and at 1-, 3-, and 6-months post-training. Organizational data will be collected at baseline, 1-, 3-, and 6-months post training, while patient data will be collected at baseline and 6-months post training. Discussion: This study will develop and evaluate a CCI consisting of a tablet-based mobile platform for treatment providers, an interagency communication protocol, and a training protocol as a means of improving the integration of care for PLWH who have a SUD. Results have the potential to advance the field by bridging gaps in a fragmented healthcare system, and improving treatment efficiency, work flow, and communication among interdisciplinary providers from different treatment settings.