The lack of affordable mineral fertilizers and scarcity of organic materials cause decline in soil fertility for smallholder farmers and producers in the highlands of Madagascar, challenging crop productivity. To fulfill plant growth and nutrition, we explored the effect of 132 combinations of 17 different fertilizing resources, both organic and mineral, on rice growth and nutrition using a greenhouse experiment. Two clustering approaches were used to evaluate the effects of fertilizing resources: elemental clustering and functional clustering. Elemental clustering grouped resources based on their elemental intrinsic composition, while functional clustering grouped resources based on their effect in improving plant growth and nutrition when combined in soil. We found that some resources closely grouped based on their elemental composition exhibited different effects on plant growth and nutrition when combined in soil. Zebu horn emerged as a particular organic resource in elemental clustering, and a key resource in functional clustering by promoting plant growth and nutrition when combined with other resources in soil. Its unique elemental composition played a significant role in driving positive interactions with other resources. We proposed to extend the concept of ‘assembly motif’ within soil fertilization strategy, suggesting that the combination of functional groups of resources determines better their fertilizing effect than their elemental composition. Resources inducing high interaction effects should be combined with those having high elemental composition to optimize crop productivity.