Luminosity distance estimates from electromagnetic and gravitational wave sources are generally different in models of dynamical dark energy and gravity beyond the standard cosmological scenario. We show that this leaves a unique imprint on the angular power-spectrum of fluctuations of the luminosity distance of gravitational-wave observations which tracks inhomogeneities in the dark energy field. Exploiting the synergy in supernovae and gravitational wave distance measurements, we build a joint estimator that directly probes dark energy fluctuations, providing a conclusive evidence for their existence in case of detection. Moreover, such measurement would also allow to probe the running of the Planck mass. We discuss experimental requirements to detect these signals.