Low yields of East African highland bananas (Musa spp. AAA-EA) are often attributed to poor and declining soil fertility, which outweighs other biophysical factors and management practices. We investigated the influence of planting density on nutrient mass fractions and nutrient imbalance indices in bananas under small-scale, low-input systems using the compositional nutrient diagnosis (CND) approach. Boundary line functions were developed to identify yield limiting factors and quantify their contribution to the yield gap. Soil, plant, yield and water data were collected in plant density experiments conducted in three contrasting agro-ecological sites of Rwanda (i.e. Kibungo low rainfall with medium soil fertility, Rubona high rainfall but low soil fertility and Ruhengeri high rainfall with high soil fertility). Effects of site × cultivar and site × density on bunch yield were significant (p < 0.05). Annual yields (t ha−1 yr−1) ranged from 6.1 to 9.2 at Kibungo, 9.5 to 21.5 at Rubona and 7.0 to 25.0 at Ruhengeri. Similar trends were registered for the above ground dry matter yield. CND indices showed that K, Mg and P were the most deficient elements in areas with low inherent soil fertility (Kibungo and Rubona). The yield gap analysis also confirmed that K was the most limiting factor, contributing to a predicted yield gap of 55.3% at Kibungo while P and Mg collectively contributed to a 35% yield gap at Rubona. An increase in plant density resulted in an increase in average yield gap from 45.6 to 70.2% at Kibungo, whilst the average yield gap decreased significantly with increases in plant density from 47.5 to 30.2% at Rubona and 76.6 to 53.7% at Ruhengeri. The study confirmed that soil fertility is a more limiting factor than water, but both CND norms and boundary line analysis showed that predicted yield gaps seem to be higher for plant density than soil fertility. Therefore, plant density management is an entry point to optimize yield of East African highland bananas