In this paper, we present a convergent collocation method with which to find the numerical solution of a generalized fractional integro-differential equation (GFIDE). The presented approach is based on the collocation method using Jacobi poly-fractonomials. The GFIDE is defined in terms of the B-operator introduced recently, and it reduces to Caputo fractional derivative and other fractional derivatives in special cases. The convergence and error analysis of the proposed method are also established. Linear and nonlinear cases of the considered GFIDEs are numerically solved and simulation results are presented to validate the theoretical results.