BackgroundCaesarean section (CS) rates are rising. Shared decision making (SDM) is a component of patient-centered communication which requires adequate information and awareness. Women in Ghana have varying perceptions about the procedure. We sought to explore mothers’ knowledge. perceptions and SDM-influencing factors about CSs.MethodsA transdisciplinary mixed-methods study was conducted at the maternity unit of Korle-Bu Teaching Hospital in Accra, Ghana from March to May, 2019. Data collection was done in four phases: in-depth interviews (n= 38), pretesting questionnaires (n= 15), three focus group discussions (n= 18) and 180 interviewer administered questionnaires about SDM preferences. Factors associated with SDM were analyzed using Pearson’s Chi-square test and multiple logistic regression.ResultsMothers depicted a high level of knowledge regarding medical indications for their CS but had low level of awareness of SDM. The perception of a CS varied from dangerous, unnatural and taking away their strength to a life-saving procedure. The mothers had poor knowledge about pain relief in labour and at Caesarean section. Health care professionals attributed the willingness of mothers to be involved in SDM to their level of education. Husbands and religious leaders are key stakeholders in SDM. Insufficient consultation time was a challenge to SDM according to health care professionals and post-partum mothers. Women with parity ≥ 5 have a reduced desire to be more involved in shared decision making for Caesarean section. AOR = 0.09, CI (0.02–0.46).ConclusionThere is a high knowledge about the indications for CS but low level of awareness of and barriers to SDM. The fewer antenatal care visits mothers had, the more likely they were to desire more involvement in decision making. Aligned to respectful maternity care principles, greater involvement of pregnant women and their partners in decision making process could contribute to a positive pregnancy experience. Education, including religious leaders and decision- making tools could contribute to the process of SDM.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12884-023-05739-7.