Low- and middle-income countries shoulder the greatest burden of stunting and anaemia in children. This calls for prompt and effective intervention measures, while the contributing factors are not fully understood. This study evaluates determinants spanning from individual-, household- and community levels including agroecology and antinutrients as unique sets of predictors. Primary data were collected from 660 rural households representing the midland (ML), highland, and upper highland (UHL) agroecological zones from northern Ethiopia. The study relates several predictors to stunting and anaemia in children aged 6-23 months. We found 49.1% and 49.7% of children were stunted and anaemic, respectively. Children living in the ML are approximately twice more likely to be stunted adjusted odds ratio (AOR: 1.869; 95% CI: 1.147-3.043) than in the UHL. The risk of stunting increases by 16.3% and 41.9% for every unit increase in phytate-to-zinc and phytate-to-iron molar ratios, respectively. A 10% increase in mean aggregated crop yield was observed to reduce the likelihood of stunting occurrence by 13.6%. Households lacking non-farm income-generating opportunities, travel longer time to access the marketplace and poor health service utilisation were associated with increased risk of stunting. Low diversity of child's diet, age of the child (18-23 months) and mothers at a younger age are significantly associated with stunting. Risk of anaemia in children is high amongst households with unimproved water, sanitation, and hygiene practices, younger age (6-11 months) and mostly occurs amongst boys. Children in the ML had a 55% reduced risk of being anaemic (AOR: 0.446; 95% CI: 0.273-0.728) as compared to the UHL. Therefore, the influence of these factors should be considered to tailor strategies for reducing undernutrition in children of 6-23 months in rural Ethiopia. Interventions should go beyond the administrative boundaries into targeting agroecological variation.