Ecological communities encompass rich diversity across multiple trophics. While modern coexistence theory has been useful in understanding community assembly, its traditional formalism only allows for the study of assembly within a single trophic level. Here, using an expanded definition of niche and fitness differences applicable to multi-trophic communities, we study how diversity within and across trophics affect species coexistence. Specifically, we investigate how assembly in one trophic level impacts the coexistence of three types of communities: (1) the single-trophic subcommunity with species at that level, (2) the single-trophic subcommunity with species at an adjacent level, and (3) the entire multitrophic community. We find that while coexistence mechanisms are similar for single-trophic communities, they differ for multitrophic ones. We also find that fitness differences primarily constrain diversity in lower-level tropics, while niche differences primarily constrain diversity in higher-level tropics. Empirical data corroborates our predictions about multitrophic structures. Our work provides needed theoretical expectation of multitrophic communities within modern coexistence theory.