Despite intense, long-term interest in organic semiconductors from both an applied and fundamental perspective, key aspects of the electronic properties of these materials remain poorly defined. A particularly challenging problem is the molecular nature of positive charge carriers, that is, holes or oxidized species in organics. Here, the unique ability of single-molecule spectroelectrochemistry (SMS-EC) to unravel complex electrochemical process in heterogeneous media is used to study the oxidation of nanoparticles of the conjugated polymer poly(9,9-dioctylfluorene-co-benzothiadiazole). A reversible hole-injection charging process has been observed that occurs primarily by initial injection of shallow (untrapped) holes, but soon after the injection, a small fraction of the holes becomes deeply trapped. Good agreement between experimental data and simulations strongly supports the presence of deep traps in the studied nanoparticles and highlights the ability of SMS-EC to study energetics and dynamics of deep traps in organic materials at the nanoscale.