In this article, the numerical solution of the mixed Volterra–Fredholm integro-differential equations of multi-fractional order less than or equal to one in the Caputo sense (V-FIFDEs) under the initial conditions is presented with powerful algorithms. The method is based upon the quadrature rule with the aid of finite difference approximation to Caputo derivative usage collocation points. For treatments, our technique converts the V-FIFDEs into algebraic equations with operational matrices, some of which have the symmetry property, which is simple for evaluating. Furthermore, numerical examples are presented to show the technique’s validity and usefulness as well comparisons with previous results. The majority of programs are performed using MATLAB v. 9.7.