Malnutrition is viewed as one of climate change’s five most considerable adverse health impacts. This study, from a drought-and famine-prone food insecure setting in the Rift Valley of southern Ethiopia, aims to quantify the possible causal effect of climate variation on women’s nutritional status through its effect on the normalized difference vegetation index (NDVI), a proxy measure for crop production, and household food security. Using a cohort study design, we ensured a temporal relationship between the main exposures preceding the mediator and the outcome. Women living in 904 households from nine randomly selected subsistence farming in rural Kebeles, the lowest administrative unit in the Boricha district in Sidama, were visited quarterly to collect nutritional status (outcome variable), household food security status (HHFS), and sociodemographic information. Climate data (rainfall and temperature) was obtained from the Google Earth Engine. Generalized structural equation modeling (GSEM) was used to measure the association between rains, the NDVI, and women’s nutritional status after adjusting for the mediation effect of HHFS. The analysis adjusted the clustering effect of Kebele and the household. The study showed that the NDVI and HHFS directly affected women’s body mass index. Moreover, household heads who attended primary education, total energy expenditure of women, and household wealth were positively associated with women’s BMI. On the other hand, older women and women who were not members of a community-based health insurance had a lower BMI. Climate variability, NDVI, and household food security could be causally linked to women’s nutritional status, suggesting that rural people depending on rain-fed subsidence farming for crop production are vulnerable to the impact of climate variability.