Introduction: Universally, malaria continues to ravage the lives of innocent expectant women. In Kenya malaria prevalence among adult females is 28% while in Mt. Elgon Sub County, which is categorised under highland epidemic prone malaria area, prevalence of malaria in pregnancy (MiP) is uncertain. Therefore, this study sought to determine intriguing predictors associated with malaria infection among pregnant women in Mt. Elgon Sub-County. Methods: Cross-sectional analytical design was employed and mixed methods used for data collection. For quantitative data collection, semi-structured questionnaire was used to collect primary data from pregnant women who attended ANC in selected health facilities in the study area. Further, qualitative approach adopted interview guides that targeted key informants in the health facilities. Systematic random sampling method was used to select 392 participants for the study. Data was analysed by SPSS version 25.0.  Bivariate logistic regression analysis was used to test the association between independent variable and dependent variable. Findings:  Study results revealed that, the prevalence of MiP was 16.2%. Prevalence was higher among women aged less than 25 (67.3%, n=262) compared to those aged > 25 years (33.7%, n=137). The following five factors were statistically significantly associated with malaria prevalence in pregnancy: place of residence (OR: 5.7; 95%CI: 2.6 – 12.4; p < 0.0001); those who tested positive in the last 2 years (OR: 1.7; 95%CI: 1.0 – 2.9; p = 0.05); preferred shape of ITN’s (OR: 3.8; 95%CI: 1.5 – 9.7; p = 0.008);earth floor (OR: 1.8; 95%CI: 1.0 – 3.1; p = 0.03);  mud wall (OR: 1.8; 95%CI: 1.0 – 3.1; p = 0.03). In conclusion, age group, place of residence, testing positive in the last 2 years, preferred shape of ITN, earth floor and mud wall were significant factors associated with MiP. Recommendations: To curb MiP, the study recommends Bungoma County government to promote use of ITNs and preferable rectangular ITN’s by ensuring they are translated to appropriate use; support regular indoor residual spraying with insecticides and educate the residents on the role of improved housing on malaria protection and empowerment of the community to adopt improved housing.