<p>This study investigates a three-species food chain model comprising of a prey, an intermediate predator, and a top predator using Caputo fractional order derivatives. In the proposed model, the prey grows logistically while experiencing Allee effect. Holling type II functional responses are used to represent interactions between prey and intermediate predators, as well as between intermediate predators and top predators. Numerical simulations of the proposed model are performed in traditional integer order model along with fractional order models, with and without exposing the prey population to the Allee effect. It is found that the presence of the Allee effect plays a positive role in the coexistence of all species under the restricted conditions of the parameters. Without Allee effect in prey population, all populations show chaotic behavior in integer order model, but introduction of the weak Allee effect in prey population allows the stable coexistence of all three populations in all models fractional as well as in integer order models and the populations which fail to coexist in the integer model can coexist in the fractional order models even when prey are subjected to strong Allee effect. Theorems like existence and uniqueness, positivity, and uniform boundedness of the solutions are proved. The local and global stability of all equilibrium points is investigated.</p>