In mixed tree‐grass ecosystems, tree recruitment is limited by demographic bottlenecks to seedling establishment arising from inter‐ and intra‐life‐form competition, and disturbances such as fire. Enhanced nutrient availability resulting from anthropogenic nitrogen (N) and phosphorus (P) deposition can alter the nature of these bottlenecks by changing seedling growth and biomass allocation patterns, and lead to longer‐term shifts in tree community composition if different plant functional groups respond differently to increased nutrient availability. However, the extent to which tree functional types characteristic of savannas differ in their responses to increased N and P availability remains unclear. We quantified differences in above‐ and belowground biomass, and root carbohydrate contents in seedlings of multiple N‐fixing and non‐N‐fixing tree species characteristic of Indian savanna and dry forest ecosystems in response to experimental N and P additions. These parameters are known to influence the ability of plants to compete, as well as survive and recover from fires. N‐fixers in our study were co‐limited by N and P availability, while non‐N‐fixers were N limited. Although both functional groups increased biomass production following fertilization, non‐N‐fixers were more responsive and showed greater relative increases in biomass with fertilization than N‐fixers. N‐fixers had greater baseline investment in belowground resources and root carbohydrate stocks, and while fertilization reduced root:shoot ratios in both functional groups, root carbohydrate content only reduced with fertilization in non‐N‐fixers. Our results indicate that, even within a given system, plants belonging to different functional groups can be limited by, and respond differentially to, different nutrients, suggesting that long‐term consequences of nutrient deposition are likely to vary across savannas contingent on the relative amounts of N and P being deposited in sites.