The possibility that some ecosystems can exist in alternative stable states has profound implications for ecosystem conservation and restoration. Current ecological theory on multistability mostly relies on few-species dynamical models, in which alternative states are intrinsically related to specific non-linear dynamics. Recent theoretical advances, however, have shown that multiple stable ‘cliques’—small subsets of coexisting species—can be present in species-rich models even under linear interactions. Yet, the mechanisms governing the appearence and characteristics of these cliques remain largely unexplored. In the present work, we investigate cliques in the generalized Lotka–Volterra model with mathematical and computational techniques. Our findings reveal that simple probabilistic and dynamical constraints can explain the appearence, properties and stability of cliques. Our work contributes to the understanding of alternative stable states in complex ecological communities.