Coherent control of single quantum systems in complex environments has great potential to manipulate and understand photoinduced chemical and biological processes on a molecular level. However, heterogeneous environments usually impede full control and complicate interpretation. Here, we demonstrate photoluminescence-detected ultrafast phase-only coherent control on single organic molecules in a disordered matrix at room temperature. Combined with a multiparameter quantum dynamics identification procedure, we reconstruct multiphoton processes and energy landscapes for each molecule. We find strong phase dependencies of the corresponding transitions into highly excited states. Importantly, also transitions into hidden states, which are not connected to photoluminescent channels, are monitored and controlled. Our combined approach provides a general toolbox to manipulate and understand ultrafast photoinduced processes in single quantum systems, which is a prerequisite to control chemical and biological function.