With increasing biodiversity loss occurring worldwide, there is a need to understand how these losses will affect ecosystem structure and function. Biodiversity loss leads to changes in species interactions and alters the trophic complexity of food webs. These alterations to trophic complexity can be described by changes to the diversity of food resources and the diversity of trophic levels. To understand how biodiversity affects the trophic complexity of food webs, we used 10 islands across the Aleutian Archipelago to compare the alternate state communities found in kelp forest ecosystems (kelp forest and urchin barren communities) and then compared these to natural reference communities without local benthic production (their associated offshore communities). We constructed food webs for each community across the Aleutian Archipelago using primary producer and consumer carbon (d13C, a proxy for food sources to a consumer) and nitrogen (d15N, a proxy for consumer trophic level) stable isotope values. Our findings suggest that biodiversity loss (i.e., the phase change from kelp forest to urchin barren) leads to reductions in trophic complexity, which was similar to naturally occurring communities with low local resource biodiversity. This was expressed by lower consumer isotopic dietary niche areas, especially omnivores and herbivores, and lower omnivore and carnivore trophic levels within the urchin barren communities. We clarify how biodiversity promotes food resources and increases trophic levels and complexity through critical trophic conduits.