Inhomogeneous cosmological perturbation equations are derived in loop quantum gravity, taking into account corrections, in particular, in gravitational parts. This provides a framework for calculating the evolution of modes in structure formation scenarios related to inflationary or bouncing models. Applications here are corrections to the Newton potential and to the evolution of large scale modes which imply nonconservation of curvature perturbations possibly noticeable in a running spectral index. These effects are sensitive to quantization procedures and test the characteristic behavior of correction terms derived from quantum gravity.