Despite South Africa having a progressive and liberal sexual and reproductive health (SRH) policy framework, adolescents and young people with disabilities (AYPWDs) are less likely to receive sexual and reproductive healthcare, being consequently predisposed to a long-term detrimental impact on their health. Our study explored the barriers to accessing sexual and reproductive health services (SRHSs) in clinics among AYPWDs in Mpumalanga, South Africa. We conducted a descriptive qualitative study with twenty-seven AYPWDs in four focus group discussions using semi-structured interviews, audiotaped and transcribed verbatim, and then applied a thematic analysis of the data. Employing a socio-ecological model, the findings show a poor socioeconomic status, lack of information on SRH, and the attitudes of AYPWDs as barriers at the individual level, hindering AYPWDs from accessing SRHSs in clinics. AYPWDs also faced difficulties to talk about SRH with parents, a lack of support to seek SRHSs, improper care from family/parents, and negative attitudes of friends, at the interpersonal level. They further expressed barriers at the community/societal level as negative attitudes of non-disabled community members and poor infrastructure for wheelchair use. At the organization level, their access to SRHSs was negatively affected by HCWs’ maltreatment, described in the forms of negative attitudes, being judgmental using verbal abuse, discrimination, and bullying. Furthermore, AYPWDs described difficulties in communication with HCWs, as well as violating their confidentiality and misconceived ideas on their sexuality. Intensified efforts to strengthen public health strategies are needed to improve access to SRHSs by AYPWDs in South Africa, as well as enhancing the proficiency and communication skills of HCWs and educating AYPWDs, parents, and non-disabled community members on SRH.