In tree-based agroecosystems, environmental heterogeneity can be high and resource acquisition strategies among individual plants can be expected to vary. This poses a challenge for appropriate nutrient prescriptions. We used a novel trait-based approach to measure in situ fine root phenotypic response of cocoa (Theobroma cacao) to fertilization. Two levels of NPK fertilizer were applied to cocoa in agroforestry, with shade trees Entandrophragma angolense or Terminalia ivorensis, or in monoculture. Four months following fertilization, cocoa fine roots were extracted from ingrowth cores and analyzed for a suite of traits positively associated with resource acquisition: fine root production, ratio of absorptive to transport roots, specific root length, specific root area, specific root tip abundance, and root nitrogen content, as well as traits positively associated with longer-lived root organs (resource conservative): root tissue density, average root diameter, and root carbon to nitrogen ratio. In surface soils (0 to 10 cm), fertilization largely stimulated roots to express resource conservative strategies compared to unfertilized cocoa roots (up to 70% mean percent difference among all root traits) but with limited measurable differences in root trait response between the two fertilization levels. In subsurface soils (10 to 20 cm), however, inconsistent cocoa root responses to fertilization and shade trees suggested increasing complexity in nutrient acquisition strategies with soil depth. At both depths, we detected coordination among cocoa root trait variation including a resource acquisition to conservation axis explaining~45% of total trait variation, yet an individual cocoa plant's position on these coordinated trait axes was predominately affected by the shade tree rather than fertilization level. This study provides some of the first insights into intraspecific root functional trait expression to fertilization in multispecies agriculture. We show that a trait-based approach can be used to improve diagnostics and prescriptions of nutrient amendments in agroforestry systems.