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Introduction There is a need to assess and strengthen reproductive rights-based family planning and abortion services in Indian medical schools that play a key role in medical education and service delivery. This study presents the findings of baseline assessment across nine schools in two states and one union territory with objective to assess, identify the gaps and improve the status of reproductive rights and evidence-based family planning and abortion services in Indian medical schools. Methods A convergent parallel mixed methods study was conducted in nine medical schools in Rajasthan, Gujarat, and Chandigarh a Union territory in India from October 2018 to June 2019. In-depth interviews with 33 faculty from the Department of Obstetrics and Gynaecology were conducted. The COM-B (Capability, Opportunity, and Motivation) model of behaviours was used to qualitatively identify barriers and facilitators of reproductive rights-based family planning and abortion services. Reproductive health services provided to 104 women for family planning and abortion were observed quantitatively using a pre-tested checklist. Findings Providers’ preference bias in recommending contraceptive methods to specific clients (wherein sterilisation was offered to women with two or more children and IUCD to women with one child) was observed as barrier to reproductive rights. The facilitators of rights based reproductive services included well-informed faculty regarding providing dignified and respectful care. Barriers included infrastructure gaps, high workload, insufficient human resources affecting privacy, and lower awareness and decision-making power of clients. Family planning counselling using the cafeteria approach was offered in 69.4% of cases, 31.6% of women seeking abortion services were offered counselling on both family planning and abortion. Sterilisation or IUD insertion was a pre-condition in 36.8% of women requesting an abortion. Conclusions Right-based reproductive services around family planning counselling and abortion services were delivered partially despite the medical schools’ trained faculty, mainly due to provider bias, high workload, and less autonomy and lower awareness of reproductive rights among women.