Backgrounds Micronutrient deficits in women of reproductive age have been linked to poor pregnancy outcomes. The most common micronutrient deficits in women are iron and folate. The World Health Organization recommends daily oral iron and folic acid supplementation (IFAS) as part of routine antenatal care to lower the risk of maternal anemia and adverse pregnancy outcomes. However, the effectiveness of the supplementation relies on client’s strict adherence. The aim of this study was to determine time- to- non-adherence to IFAS and associated factors among pregnant women in Hosanna Town, South Ethiopia. Methods A community based cross sectional study design was employed from May 15-June11, 2021. Data were entered into Epi-Data version 3.1 and exported to SPSS version 23 for analysis. The Cox regression hazard model was applied. The threshold of statistical significance was declared at a p-value <0.05 and adjusted hazard ratios (AHRs) with corresponding 95% confidence intervals were used to report. Result The median time-to-non-adherence was 74 days (95 percent CI: 65.33–82.67). After adjusting for the confounders, age (AHR = 1.05, 95% CI: 1.01–1.09), education status (AHR = 2.43 95%CI 1.34–4.40, AHR 3.00, 95% CI: 2.09–4.31, AHR 1.91, 95% CI: 1.32–2.77), household’s wealth index (AHR = 1.73, 95% CI: 1.19–2.51, AHR = 1.64, 95% CI:1.15–2.35), and counseling at service delivery (AHR = 2.53, 95% CI: 1.88–3.41) were independent predictors of time to non-adherence to IFAS among pregnant women. Conclusion The median time to non-adherence was short and women became non-adherent before the recommended duration. Improving women’s education and counseling pregnant women on IFAS during pregnancy would make a change.