Here we present a comprehensive study on the photophysics of QDs-fullerene blends, aiming to elucidate the impact of ligands on the extraction of carriers from QDs. We investigated how three different ligands (oleylamine, octadecanethiol and propanethiol) influence the dynamics of charge generation, separation, and recombination in blends of CdSe/CdS core/shell QDs and PCBM. We accessed each relevant process directly by combining the results from both optical and magnetic spectroscopies. Transient absorption measurements revealed a faster interaction dynamics in thiol-capped ligands. Through phenomenological modeling of the interaction processes, i.e., energy transfer and electron transfer, we estimated the suppression of exciton migration and the enhancement of electron transfer processes when alkyl-thiols are employed as ligands. Contextually, we report the profound impact of the ligands' alkyl chain length, leading to strengthened interactions with PCBM acceptors. Quantitatively, we measured a 10-fold increase in the electron transfer rate when oleylamine ligands were exchanged with propanethiol ligands. EPR spectroscopy gave access to subtle details regarding both the enhanced charge generation and lower binding energy of charge-transfer states in blends compared to PCBM alone. Moreover, through pulsed EPR techniques, we inferred the localization of deep electron traps in localized sites close to QDs in the blends. Therefore, our thorough characterization evidenced the essential role of ligands in determining QD interactions. We believe that these discoveries will contribute to the efficient incorporation of QDs in existing organic PV technologies.