Significance Monitoring the real-space motion of the electrons directly involved in ultrafast molecular dynamics is a challenging goal, hindered by the strong contributions of the remaining inactive electrons. Molecular quantum coherences can provide a direct window into elementary electronic dynamics, but they could not be separately imaged so far. Here, we demonstrate a time- and frequency-resolved X-ray diffraction technique, which can employ existing stochastic X-ray pulses to separately image the coherence contributions. The technique can selectively follow the relevant electrons involved in the ultrafast dynamics and identify the confined molecular regions covered by their motion. It enables readily feasible measurements and can be straightforwardly extended to full three-dimensional imaging via X-ray and electron diffraction.