We present a method for the generation and coherent manipulation of pulsed quantum frequency combs. Until now, methods of preparing high-dimensional states on-chip in a practical way have remained elusive due to the increasing complexity of the quantum circuitry needed to prepare and process such states. Here, we outline how high-dimensional, frequency-bin entangled, two-photon states can be generated at a stable, high generation rate by using a nested-cavity, actively mode-locked excitation of a nonlinear micro-cavity. This technique is used to produce pulsed quantum frequency combs. Moreover, we present how the quantum states can be coherently manipulated using standard telecommunications components such as programmable filters and electro-optic modulators. In particular, we show in detail how to accomplish state characterization measurements such as density matrix reconstruction, coincidence detection, and single photon spectrum determination. The presented methods form an accessible, reconfigurable, and scalable foundation for complex high-dimensional state preparation and manipulation protocols in the frequency domain.