A high-order linear q-difference equation with polynomial coefficients having q-Hahn multiple orthogonal polynomials as eigenfunctions is given. The order of the equation coincides with the number of orthogonality conditions that these polynomials satisfy. Some limiting situations when are studied. Indeed, the difference equation for Hahn multiple orthogonal polynomials given in Lee [J. Approx. Theory (2007), ), doi: 10.1016/j.jat.2007.06.002] is obtained as a limiting case.