Background With a fertility rate of 5.4 children per woman, Burundi has been ranked as seventh highest country with the highest fertility rate in the world. Family planning is known to allow couples to achieve the desired family size, appropriate space birth and the limitation of pregnancies. Also, family planning can contribute to mitigating some health issues such as unintended pregnancies and abortions all of which, are often associated with multi-parity. In conservative community in rural Burundi, knowledge on family planning is high and such services are free yet utilisation is low. Employing a mixed methods, this study first quantifies contraceptive prevalence and second, explore the contextual multilevel factors associated with low family planning utilisation among married women.Methods An explanatory sequential mixed study was conducted. Five hundred and thirty women in union were interviewed using structured and pre-tested questionnaire. Next, 11 focus group discussions were held with community members composed of married men and women, administrative and religious leaders (n=132). The study was conducted in eighteen collines of two health districts of Vyanda and Rumonge in provinces of Bururi and Rumonge respectively. Quantitative data was analysed with SPSS and qualitative data was coded and deductive thematic methods were applied to find themes and codes.Results The overall contraceptive prevalence was 22.6%. Injectables (40%), Implants (24.6%), Male condom (10.8%) and pills (6.2%) were the major contraceptive methods utilized by study participants. Factors inhibiting family planning use emanated from a range of issues which were identified during the qualitative phase. Notable among those was experiencing side effects and costs associated with its management in the health system. Religious conceptualisation and ancestral negative beliefs of family planning had also shaped how people perceived it. Furthermore, at the household level, gender imbalances between spouses had resulted in break in communication, also serving as a factor for non-use of family planning. Conclusion The study suggests that low uptake of family planning can be attributed to perceived or experienced side effects as well as deeply rooted negative beliefs which are reinforced by religious beliefs. Men and religious leaders’ involvement in family planning initiatives can positively impact behaviour change and increase family planning acceptance.