Background Micronutrient (MN) deficiency among children is recognised as a major public health problem in Ethiopia. The scarcity of MNs in Ethiopia, particularly in pastoral communities, might be severe due to poor diets mitigated by poor healthcare access, drought, and poverty. To reduce MNs deficiency, foods rich in vitamin A (VA) and iron were promoted and programs like multiple micronutrient powder (MNP), iron and vitamin A supplements (VAS) and or deworming have been implemented. Nationally for children aged 6-23 months, consumption of four or more food groups from diet rich in iron and VA within the previous 24 hours, MNP and iron supplementation within seven days, and VAS and 75% of deworming within the last 6 months is recommend; however, empirical evidence is scarce. Therefore, this study aimed to assess the recommended MN intake status of children aged 6-23 months in the emerging regions of Ethiopia. Methods Data from the Ethiopia Demographic and Health Survey 2016 were used. A two-stage stratified sampling technique was used to identify 1009 children aged 6-23 months. MN intake status was assessed using six options: food rich in VA or iron consumed within the previous 24 hours, MNP or iron supplementation with the previous seven days, VAS or deworming within six months. A multilevel mixed-effect logistic regression analysis was computed, and a p-value of Results In this analysis, 37.3% (95% CI: 34.3-40.3) of children aged 6-23 months had not received any to the recommended MNs sources. The recommended MNs resulted; VAS (47.2%), iron supplementation (6.0%), diet rich in VA (27.7%), diet rich in iron (15.6%), MNP (7.5%), and deworming (7.1%). Antenatal care visit (AOR: 1.9, 95% CI: 1.4-2.8), work in the agriculture (AOR: 2.2, 95% CI: 1.3-3.8) and children aged 13 to 23 months (AOR: 1.7, 95% CI: 1.2-2.4) were the individual-level factors and also Benishangul (AOR: 2.2, 95% CI: 1.3-4.9) and Gambella regions (AOR: 1.9, 95% CI: 1.0-3.4) were the community-level factors that increased micronutrient intake whereas residence in rural (AOR: 0.4, 95% CI: 0.1-0.9) was the community-level factors that decrease micronutrient intake. Conclusions Micronutrient intake among children aged 6-23 months in the pastoral community was low when compared to the national recommendation. After adjusting for individual and community level factors, women's occupational status, child's age, antenatal visits for recent pregnancy, residence and region were significantly associated with the MN intake status among children aged 6-23 months.