Urban and peri-urban agriculture (UPA) is important for food security in fast growing cities of developing countries. UPA also may have an important role in nutrient re-cycling at the interface of rural and urban areas. However, little is known about this role and whether it is different for different UPA systems. Here, we report on diversity and nutrient balances of UPA systems in three main cities of Ethiopia. Data collected from 425 households (Addis Ababa: 175, Adama: 126 Jimma: 124) were subjected to categorical principal component analysis and cluster analysis to classify the households. Four farm types per city and overall six: commercial livestock (cLS), commercial vegetable crop (cVC), subsistence field crop (sFC), cLScVC, cLScVCsFC and sVCsFC were identified across the three cities. Two types, cLS and cLScVC were common to the three cities. The farm types differed in resource endowment, income, soil fertility management and nutrient balances. cLS systems accumulated 450, 85 and 260 kg N, P and K ha−1 year−1 and had 26% N and P and 15% K use efficiency, respectively while sFC systems depleted − 30 kg N and − 17 kg K ha−1 year−1 and had 155% N and > 100% K use efficiency. There was little exchange of manure and crop residue between LS, FC and VC systems. To use the potential role of UPA in nutrient re-cycling, a directive that imposes LS systems to distribute their surplus manure resources to proximate FC and VC systems and improve their nutrient use efficiency should be put in place.