In this research, by utilizing the concept of the mixed Caputo fractional derivative and left-sided mixed Riemann–Liouville fractional integral, we approximate the solution of generalized fractional Benjamin–Bona–Mahony–Burgers equations (GF-BBMBEs). In addition, using Genocchi polynomial properties, we obtaina new formula to approximate the functions by Genocchi polynomials. In the process of computation, we discuss a method of obtaining the operational matrix of integration and pseudo-operational matrices of the fractional order of derivative. Also, an algorithm of obtaining the mixed fractional integral operational matrix is presented. Using the collocation method and matrices introduced, the proposed equations are converted to a system of nonlinear algebraic equations with unknown Genocchi coefficients. In addition, we discuss the upper bound ofthe error for the proposed method. Finally, we examine several problems to demonstrate the validity and applicability of the proposed method.