Coherence is a key aspect of a large variety of processes, ranging from the coherent delocalisation of excitation energy, which is important for energy transfer in supramolecular nanostructures, to coherence between electronic states of a single quantum system, which is essential for quantum optical applications. Coherent control schemes exploit this quantum mechanical property by actively manipulating the outcome of dynamical processes. Moreover, this technique allows measuring dynamical processes under the influence of dephasing. However, going beyond the ensemble averaged situation, i.e. working on the level of single quantum systems, is highly challenging for quantum systems embedded in a solid matrix at elevated temperature. Since interactions between the quantum system and its specific local environment are a priori unknown, this requires a reliable approach to retrieve the relevant parameters governing the ultrafast coherent dynamics. Here, we present measurements of the ultrafast coherence decay of two-photon accessible excited states in single organic molecules embedded in a disordered environment at room temperature. We combine this experimental approach with a quantum dynamics identification procedure, which yields a minimum three-level model to describe the obtained data with very good agreement. In particular, we are able to retrieve the ultrafast (coherent) excited state dynamics in single molecules and demonstrate its sensitivity to the local nanoenvironment from molecule to molecule. This work provides a robust approach to measure and analyse ultrafast quantum dynamics in complex nanosystems.