We provide a comprehensive study of the capabilities of modulated electron wavefunctions for the preparation and readout of the quantum state of the quantum emitters (QEs) they interact with. First, we consider perfectly periodic electron combs, which do not produce QE-electron entanglement, preserving the purity of the QE state while inducing Rabi-like dynamics in it. We extend our findings to more realistic, nonideally modulated electron wave packets, showing that the phenomenology persists, and exploring their use to prepare the emitter in a desired quantum state. Thus, we establish the balance that electron comb size, emitter radiative decay, and electron-emitter coupling strength must fulfill in order to implement our findings in experimentally feasible platforms. Then, moving into the limit of small electron combs, we reveal that these wavefunctions allow for quantum state tomography of their target, providing access not only to the populations, but also the coherences of the QE density matrix. Finally, we explore the realistic range of coupling strength values and the limit of validity of our treatment in the case of free electron-QE interaction being mediated by free space and in inverse-designed waveguide structures, demonstrating that our treatment remains valid for large coupling strengths in these systems. We believe that our theoretical results showcase modulated free electrons as very promising tools for quantum technologies based on light-matter coupling.