While a large variety of organic and molecular materials have been found to exhibit charge memory effects, the underlying mechanism is not well-understood, which hinders rational device design. Here, we study the charge retention mechanism of a nanoscale memory system, an organic monolayer on a silicon substrate, with Au nanoparticles on top serving as the electrical contact. Combining scanning probe imaging/manipulation and density functional simulations, we observe stable charge retention effects in the system and attributed it to polaron effects at the amine functional groups. Our findings can pave the way for applications in nonvolatile memory, neuromorphic computing, and high dielectric breakdown devices.