In rural, Indigenous Guatemala, women’s healthcare is fragmented and inadequate. Our interdisciplinary, multinational research team aimed to 1) describe reproductive health in one rural Indigenous community; 2) explore contraceptive use; and 3) learn about and prioritize Indigenous Maya women’s reproductive health beliefs and needs. Our study team conducted mixed-methods surveys with 62 women, led focus groups with 20 community health workers, and analyzed data using concurrent mixed methods analysis. We found that 51% of women surveyed reported current family planning, with 33% using a biomedical method. We found high mean fertility, 6.9 live births per woman aged 40–49 (national average 4.7), with significant socioeconomic variation. We also found that poverty correlated with total fertility, while education inversely correlated. Our research found that contraceptive use had a strong association with access to healthcare and with women’s reported sexual autonomy (which we instrumentalized based on women’s answers to the question “can you refuse to have sex with your husband?”). Many women we spoke to feared contraception, specifically concerned it could cause cancer. Overall, Guatemalan Indigenous women expressed unease seeking reproductive healthcare within health systems that have historically and currently excluded and mistreated Indigenous communities. Our research documented unexplored influences on contraceptive use, including the relationship between sexual autonomy and contraception and widespread concern of cancer with contraceptive use. We conclude, moving forward, that we and other researchers should continue to collaborate with communities to improve Indigenous women’s reproductive healthcare.