Much research has been conducted on cereal-legume intercropping as a sustainable intensification (SI) practice in Eastern and Southern Africa (ESA). However, the role of inorganic fertilizers in sustainably intensifying intercropping systems has not been systematically analyzed. Therefore, the objective of the present analysis was to assess the role of inorganic fertilizer use in cereal-pigeonpea (Cajanus cajan) intercropping in terms of SI indicators, namely, yield, production risks, input use efficiency, and economic returns. The data used for this analysis were gathered from over 900 on-farm trials across Kenya, Tanzania, and Mozambique. All SI indicators assessed showed that intercropping combined with application of small amounts of inorganic fertilizers is superior to unfertilized intercrops. Fertilizer application in the intercropping system improved cereal yields by 71–282% and pigeon pea yields by 32–449%, increased benefit–cost ratios by 10–40%, and reduced variability in cereal yields by 40–56% and pigeonpea yields by 5–52% compared with unfertilized intercrops. Improved yields and reduced variability imply lowering farmers’ risk exposure and improved credit rating, which could enhance access to farm inputs. We conclude that the strategic application of small amounts of inorganic fertilizers is essential for the productivity and economic sustainability of cereal-pigeonpea intercropping under smallholder farming in ESA.