The successful transfer of nanoparticles between solvents is critical for many applications. We evaluated the impact of amphiphilic polymer composition on the size, transfer efficiency, and biocompatibility of tri-n-octylphosphine oxide/hexadecylamine-stabilized semiconductor ZnS-capped CdSe and CdS-capped CdTe(x)Se(1-x) quantum dots (QDs). We also investigated the adsorption of various proteins onto the surface of these QDs and studied the effect of surface chemistry on non-specific protein binding. The results from these studies will have implications in the design of QDs and other nanoparticles for biological and biomedical applications.