Nutritional deficiencies are a leading underlying risk factor contributing to the global burden of disease. In Pakistan, late adolescence is considered a nutritionally vulnerable period, as micronutrient requirements are increased to support maturation, and dietary staples are nutrient poor. However, there has been limited evaluation of micronutrient status beyond anemia and its determinants. Using cross-sectional data from late adolescent and young women (15–23 years) at enrolment in the Matiari emPowerment and Preconception Supplementation (MaPPS) Trial, we aimed to describe the prevalence of key micronutrient deficiencies of public health concern, and generate hierarchical models to examine associations with proxies for social determinants of health (SDoH). The prevalence of micronutrient deficiencies was high: 53.6% (95% confidence interval (CI): 53.0–54.3%) had anemia; 38.0% (95% CI: 36.4–39.6%) iron deficiency anemia; 31.8% (95% CI: 30.2–33.3%) vitamin A deficiency; and 81.1% (95% CI: 79.8–82.4%) vitamin D deficiency. At least one deficiency was experienced by 91.0% (95% CI: 90.1–92.0%). Few SDoH were maintained in the final hierarchical models, although those maintained were often related to socioeconomic status (e.g., education, occupation). To improve the micronutrient status of late adolescent and young women in Pakistan, a direct micronutrient intervention is warranted, and should be paired with broader poverty alleviation methods.