QD–dye systems are promising models for artificial photosynthesis and down-converter systems for LEDs and displays. To better understand the factors controlling energy transfer from the QDs to the dyes, we fabricated a series of CdxZn1–xS/ZnS quantum dot (QD)-perylene diimide (PDI) composite nanocrystals. The core–shell CdxZn1–xS/ZnS QDs were chosen for better control of surface chemistry and for the control of photophysical properties through core composition. The PDIs were designed with bulky substituents to reduce dye–dye aggregation effects. Energy transfer efficiency was found to depend upon both the length of the anchoring alkyl chain and the type of the terminal anchoring group. The maximum energy transfer efficiency of 91% from QDs to PDIs was achieved with composites containing PDIs with carboxylic acid anchoring groups and longer alkyl chains. It was found that composites with carboxylic acid anchors exhibited greater photostability than composites with amine anchors. Longer alkyl chains also led to greater photostability. Conversely, shorter chain alkanes promoted faster aggregation of the nanocrystal composites.