Micronutrient deficiencies remain a public health burden among non-pregnant women in developing countries, including Nepal. Hence, this study examined micronutrient deficiencies among non-pregnant Nepalese women aged 15-49 using the 2016 Nepal National Micronutrient Status Survey (NNMSS). Data on 2143 non-pregnant women was extracted from the 2016 NNMSS. The study analysed ferritin, soluble transferrin receptor (sTfR), red blood cell (RBC) folate and zinc. Multivariable logistic analysis was carried out to assess factors associated with micronutrient deficiencies. Prevalence of ferritin, sTfR, folate, and zinc were 19%, 13%, 16% and 21%, respectively. Non-pregnant women from the Janajati region were significantly less prone to ferritin [adjusted odds ratio (AOR): 0.45; 95% confidence interval (CI): 0.25, 0.80], and those who had body mass index (BMI) of 25 kg/m2 or higher had significantly higher odds of ferritin [AOR: 2.69; 95% CI: 1.01, 7.17]. Non-pregnant women aged 35-49 years were significantly less predisposed to folate deficiency [AOR: 0.58; 95% CI: 0.40, 0.83], and the likelihood of zinc deficiency was significantly lower among non-pregnant women from richer households [AOR: 0.48; 95% CI: 0.31, 0.76]. The study provides further insight into screening high-risk subgroups and instituting public health interventions to address the prevailing micronutrient deficiencies among non-pregnant Nepalese women.