The q-Heun operator of the big q-Jacobi type on the exponential grid is defined. This operator is the most general second order q-difference operator that maps polynomials of degree $n$ to polynomials of degree $n+1$. It is tridiagonal in bases made out of either q-Pochhammer or big q-Jacobi polynomials and is bilinear in the operators of the q-Hahn algebra. The extension of this algebra that includes the q-Heun operator as generator is described. Biorthogonal Pastro polynomials are shown to satisfy a generalized eigenvalue problem or equivalently to be in the kernel of a special linear pencil made out of two q-Heun operators. The special case of the q-Heun operator associated to the little q-Jacobi polynomials is also treated.