Background Posttransplant metabolic syndrome (PTMS) is a common contributor to morbidity and mortality among solid organ transplant recipients in the late posttransplant period (≥1 year). Patients diagnosed with PTMS are at a higher risk of cardiovascular disease and frequently experience decreased physical function and health-related quality of life (HRQL). Studies in the early posttransplant period (<1 year) have shown the benefits of facility-based exercise training on physical function and HRQL, but have not evaluated the effects on metabolic risk factors. It remains unclear whether home-based exercise programs are feasible and can be delivered at a sufficient exercise dose to have effects on PTMS. This protocol outlines the methodology of a randomized controlled trial of a partly supervised home-based exercise program in lung transplant (LTx) and orthotopic liver transplant (OLT) recipients. Objective This study aims to evaluate the feasibility (ie, recruitment rate, program adherence, attrition, safety, and participant satisfaction) of a 12-week individualized, home-based aerobic and resistance training program in LTx and OLT recipients initiated 12 to 18 months after transplantation, and to assess estimates of intervention efficacy on metabolic risk factors, exercise self-efficacy, and HRQL. Methods In total, 20 LTx and 20 OLT recipients with ≥2 cardiometabolic risk factors at 12 to 18 months after transplantation will be randomized to an intervention (home-based exercise training) or control group. The intervention group will receive an individualized exercise prescription comprising aerobic and resistance training, 3 to 5 times a week for 12 weeks. Participants will meet on a weekly basis (via videoconference) with a qualified exercise professional who will supervise exercise progression, provide support, and support exercise self-efficacy. Participants in both study groups will receive a counseling session on healthy eating with a dietitian at the beginning of the intervention. For the primary aim, feasibility will be assessed through recruitment rate, program adherence, satisfaction, attrition, and safety parameters. Secondary outcomes will be measured at baseline and 12 weeks, including assessments of metabolic risk factors (ie, insulin resistance, abdominal obesity, blood pressure, and cholesterol), HRQL, and exercise self-efficacy. Descriptive statistics will be used to summarize program feasibility and effect estimates (means and 95% CIs) for sample size calculations in future trials. Results Enrollment started in July 2021. It is estimated that the study period will be 18 months, with data collection to be completed by December 2022. Conclusions A partly supervised home-based, individually tailored exercise program that promotes aerobic and resistance training and exercise self-efficacy may be an important intervention for improving the metabolic profile of LTx and OLT recipients with cardiometabolic risk factors. Thus, characterizing the feasibility and effect estimates of home-based exercise constitutes the first step in developing future clinical trials designed to reduce the high morbidity associated with PTMS. Trial Registration ClinicalTrials.gov NCT04965142; https://clinicaltrials.gov/ct2/show/NCT04965142 International Registered Report Identifier (IRRID) DERR1-10.2196/35700