We extend the generating function technique for calculation of single molecule photon emission statistics (Zheng, Y.; Brown, F. L. H. Phys. ReV. Lett. 2003, 90, 238305) to systems governed by multi-level quantum dynamics. This opens up the possibility to study phenomena that are outside the realm of purely stochastic and mixed quantum-stochastic models. In particular, the present methodology allows for calculation of photon statistics that are spectrally resolved and subject to quantum coherence. Several model calculations illustrate the generality of the technique and highlight quantitative and qualitative differences between quantum mechanical models and related stochastic approximations when they arise. Calculations suggest that studying photon statistics as a function of photon frequency has the potential to reveal more about system dynamics than the usual broadband detection schemes.