Persons who are homeless, particularly those with mental health and/or substance use disorders (MHSUDs), often do not access or receive continuous primary care services. In addition, negative experiences with primary care might contribute to homeless persons' avoidance and early termination of MHSUD treatment. The patient-centered medical home (PCMH) model aims to address care fragmentation and improve patient experiences. How homeless persons with MHSUDs experience care within PCMHs is unknown. This study compared the primary care experiences of homeless and nonhomeless veterans with MHSUDs receiving care in the Veterans Health Administration's medical home environment, called Patient Aligned Care Teams. The sample included VHA outpatients who responded to the national 2013 PCMH-Survey of Health Care Experiences of Patients (PCMH-SHEP) and had a past-year MSHUD diagnosis. Veterans with evidence of homelessness (henceforth "homeless") were identified through VHA administrative records. PCMH-SHEP survey respondents included 67,666 veterans with MHSUDs (9.2% homeless). Compared with their nonhomeless counterparts, homeless veterans were younger, more likely to be non-Hispanic Black and nonmarried, had less education, and were more likely to live in urban areas. Homeless veterans had elevated rates of most MHSUDs assessed, indicating significant co-occurrence. After controlling for these differences, homeless veterans reported more negative and fewer positive experiences with communication; more negative provider ratings; and more negative experiences with comprehensiveness, care coordination, medication decision-making, and self-management support than nonhomeless veterans. Homeless persons with MHSUDs may need specific services that mitigate negative care experiences and encourage their continuation in longitudinal primary care services.