Lactating mothers are frequently at risk for nutritional deficiencies due to the physiological requirements of lactation. Throughout the world, a significant number of lactating mothers have micronutrient intake inadequacy. Evidence on micronutrient intake during lactation is limited in rural Ethiopia. Therefore, this study aimed to determine micronutrient intake inadequacy and associated factors among lactating mothers. A community-based cross-sectional study was conducted from February 1 to 18, 2023, among lactating mothers in rural areas of the North Mecha District of Amhara Region, Northwest Ethiopia. A multistage sampling technique was used to select 449 study participants. An interviewer-administered questionnaire was employed to collect dietary intake data by using a single multiphasic interactive 24-h dietary recall. The NutriSurvey 2007 software and Ethiopia, Tanzania and Kenya food composition tables were used to calculate nutrient values for the selected 12 micronutrients. For the remainder of the analysis, SPSS version 25 was employed. The Nutrient Adequacy Ratio (NAR) and Mean Adequacy Ratio (MAR) were calculated by dividing all NAR values by the number of micronutrients computed to evaluate the nutrient intakes. A logistic regression analysis was conducted to determine the factors contributing to the overall micronutrient intake inadequacy, and statistical significance was determined at a p value <0.05. A total of 430 lactating mothers participated in the study, with a 96% response rate and a mean age of 29.46 ± 5.55 years. The overall prevalence of micronutrient intake inadequacy was 72.3% (95% CI: 67.9, 76.5). The odds of micronutrient intake inadequacy were 2.5 times higher among lactating mothers aged 18-25 years old as compared to mothers in the age group ≥36 years old (AOR = 2.52, 95% CI: 1.09, 5.83). Mothers with the educational status of unable to read and write and primary school incomplete were 3.5 (AOR = 3.49, 95% CI: 1.24, 9.83) and 3.6 (AOR = 3.56, 95% CI: 1.06, 11.99) times more likely to have micronutrient intake inadequacy than mothers with secondary school completed or above educational status, respectively. Mothers whose partner's occupation was other than farming were 3.3 times more likely to have micronutrient intake inadequacy as compared to mothers whose partners were engaged in farming (AOR = 3.32, 95% CI: 1.08, 10.27). Lactating mothers who were from food-insecure households were 83% more likely to have high micronutrient intake inadequacy as compared to lactating mothers from food-secure households (AOR = 1.83, 95% CI: 1.04, 3.23). Lactating mothers with nutrition-related unfavorable attitudes were 77% more likely to have inadequate intake of micronutrients compared to lactating mothers with favorable attitudes (AOR = 1.77, 95% CI: 1.07, 2.93). The prevalence of micronutrient intake inadequacy among lactating mothers was high. Age of the mothers, educational status of the mothers, occupation of the partner, household food security, and nutrition-related attitude were significantly associated with micronutrient intake inadequacy. Community driven nutrition education and interventions are needed to address the high micronutrient intake inadequacy among lactating mothers in rural Ethiopia.