Discerning the impact of the coherent motion of the nuclei on the timing and efficiency of charge transfer at the donor-acceptor interface is essential for designing performance-enhanced optoelectronic devices. Here, we employ an experimental approach using photocurrent detection in coherent multidimensional spectroscopy to excite a donor aromatic macrocycle and collect the charge transferred to a 2D acceptor layer. For this purpose, we prepared a cobalt phthalocyanine-graphene (CoPc-Gr) interface. Unlike blends, the well-ordered architecture achieved through the physical separation of the two layers allows us to unambiguously collect the electrical signal from graphene alone and associate it with a microscopic understanding of the whole process. The CoPc-Gr interface exhibits an ultrafast electron-transfer signal, stemming from an interlayer mechanism. Remarkably, the signal presents an oscillating time evolution modulated by coherent vibrations originating from the laser-excited CoPc states. By performing Fourier analysis on the beatings and correlating it with the Raman features, along with a comprehensive first-principles characterization of the vibrational coupling in the CoPc excited states, we successfully identify both the orbitals and molecular vibrations that promote the charge transfer at the interface.