We apply a type of background independent “polymer” quantization to a free scalar field in a flat spacetime. Using semiclassical states, we find an effective wave equation that is both nonlinear and Lorentz invariance violating. We solve this equation perturbatively for several cases of physical interest, and show that polymer corrections to solutions of the Klein-Gordon equation depend on the amplitude of the field. This leads to an effective dispersion relation that depends on the amplitude, frequency, and shape of the wave packet, and is hence distinct from other modified dispersion relations found in the literature. We also demonstrate that polymer effects tend to accumulate with time for plane-symmetric waveforms. We conclude by discussing the possibility of measuring deviations from the Klein-Gordon equation in particle accelerators or astrophysical observations.