Using a range of realistic interface geometries obtained from a molecular dynamics simulation we study the effects of different microscopic atomic arrangements on the electronic structure and charge transfer rates of the prototypical photovoltaic interface between P3HT (poly(3-hexylthiophene)) and PCBM ([6,6]-phenyl-C61-butyric acid methyl ester). The electronic structures of charge-transfer (CT) states belong to two groups that can be denoted as “charge-separated” and “charge-bridging” states. For the former group of structures, which may lead to fully separated charges, the ranges and the average values of internal reorganization energy, the electronic coupling and the charge separated states energy are evaluated. A range and distribution of absolute charge separation (CS) and recombination (CR) rates are computed using the Marcus–Levich–Jortner rate equation. Due to the variety of P3HT/PCBM interface structures, a very broad range of CS (7.7 × 109–1.8 × 1012 s−1) and CR (2.5 × 105–1.1 × 1010 s−1) “instantaneous” rates are computed. However, the energetic parameters affecting the rate evolve in time due to the dynamic nature of the interface with a characteristic timescale of about 10 ns. For this reason the slowest CR instantaneous rates are not observed and the minimum CR rate observed is determined by the rate of conformational rearrangement at the interface. The combination of these observations provides a more general framework for the interpretation of experimental spectroscopic data, suggesting that the analysis based on simple first order rates may be insufficient to describe charge transfer in organic solar cell interfaces.