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 for 2143 non-pregnant women was extracted from the 2016 NNMSS. The study analysed the levels of ferritin, soluble transferrin receptor (sTfR), red blood cell (RBC) folate, and zinc of the participants. Multivariable logistic analysis was carried out to assess factors associated with micronutrient deficiencies. The prevalence of ferritin, sTfR, folate, and zinc was observed to be 19%, 13%, 16%, and 21%, respectively. Non-pregnant women from the Janajati region were significantly less prone to high levels of 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 elevated ferritin levels [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 odds of zinc deficiency were significantly lower among non-pregnant women from wealthier households [AOR: 0.48; 95% CI: 0.31, 0.76]. This 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.