Background Despite high prevalence, food aversions are closely linked to the dietary intake of pregnant women. Thus, understanding this behavior is important in addressing the issue of maternal nutrition. Therefore, the aim of this study is to provide information on the prevalence and associated factors of food aversion and its relationship with the nutritional status of pregnant women in Boricha Woreda, Sidama Regional state, Southern Ethiopia, 2019. Methods A community based mixed cross sectional study was conducted among 505 randomly selected pregnant mothers at Boricha Woreda, Southern Ethiopia from June 1–20, 2019. Pre-tested and structured face-to-face interview questionnaire and focus group discussion guide were used to collect quantitative and qualitative data respectively. The quantitative data were cleaned, coded and entered into Epi Info version 7.1.4.0 and then exported to SPSS IBM version 20 for further analysis. The qualitative data were analyzed manually using a content analysis.The bi-variable and multivariable logistic regression was used to identify the possible factors of food aversion. AOR with the respective 95% CIs was used to declare statistical significance. Results Nearly, seven-in-ten (69.2%) of the pregnant women were averted of at least one food. Cereal (45.9%) and enset (44.2%) were averted by majority of the participants. The mean (± SD) MUAC measurement was 22.7 (± 2.4) cm. Pregnant women of age group of 24–28 [AOR = 3.04, 95% CI (1.72–5.35)] and 29–33 years [AOR = 2.00, 95% CI (1.02–3.92)], nausea during [AOR = 1.77, 95% CI (1.16–2.70)] and having additional meal [AOR = 1.68, 95% CI (1.02–2.75)] were significantly associated with food aversion. Maternal nutritional status and food aversion was sstatistically significant (p-value < 0.001). Conclusion High prevalence of food aversions (69.2%) and under nutrition (34.6%) among pregnant women is found. Therefore, the Woreda Health Office needs to intensify the integration of maternal nutrition into ANC services and training of health providers as well as critical appraisal of health extension workers should also be considered.