OBJECTIVE: To provide the details of the study protocol for an observational, case study design, implementation trial. METHODS: Implementing the DEcision-Aid for Lupus (IDEAL) study will put into practice a shared decision-making (SDM) strategy, using an individualized, culturally appropriate computerized decision-aid (DA) for lupus patients in 15 geographically diverse clinics in the USA. The overarching frameworks that guide this implementation study are the Consolidated Framework for Implementation Research (CFIR) and Powell's typology of implementation strategies. All 15 clinics will receive standardized capacity-building activities for lupus DA implementation in the clinic, including education, training, technical assistance, re-training, and incorporation of a clinic champion in the core team of each site. In addition, clinics will also choose among clinic-targeted activities to integrate the DA into existing work processes and/or patient-targeted activities to raise awareness and educate patients about the DA. These activities will be chosen to stimulate participant recruitment and retention activities that support the implementation of the DA at their clinic. In study aim 1, using surveys and semi-structured interviews with clinic personnel in 15 lupus clinics, we will assess stakeholder needs and identify clinic and contextual characteristics that inform the implementation strategy component selection and influence implementation effectiveness. Study aim 2 is to implement and assess the effectiveness of the IDEAL (standardized and tailored) strategy in 15 lupus clinics by examining the changes in our primary outcome of penetration, i.e., the proportion of all eligible patients in the clinic that receive the lupus DA, and secondary outcomes include DA appropriateness, acceptability, success, permanence, and feasibility. Study aim 3 is to identify ways to sustain and disseminate our lupus DA via semi-structured debriefing interviews with key clinic personnel and patients. DISCUSSION: The study will enroll at least 500 patient participants with lupus across all 15 sites and assess the effectiveness in implementing the DA in various clinic settings across the USA. TRIAL REGISTRATION: ClinicalTrials.gov, NCT03735238 . Protocol version number: 15, date 6/8/2020.