Among amphiphilic polymers with diverse skeletons, fluorinated architectures have attracted significant attention due to their unique property of segregation and self-assembly into discrete supramolecular entities. Herein, we have synthesized amphiphilic copolymers by grafting hydrophobic alkyl/perfluoroalkyl chains and hydrophilic polyglycerol [G2.0] dendrons onto a co-polymer scaffold, which itself was prepared by enzymatic polymerization of poly[ethylene glycol bis(carboxymethyl) ether]diethylester and 2-azidopropan-1,3-diol. The resulting fluorinated polymers and their alkyl chain analogs were then compared in terms of their supramolecular aggregation behavior, solubilization capacity, transport potential, and release profile using curcumin and dexamethasone drugs. The study of the release profile of encapsulated curcumin incubated with/without a hydrolase enzyme Candida antarctica lipase (CAL-B) suggested that the drug is better stabilized in perfluoroalkyl chain grafted polymeric nanostructures in the absence of enzyme for up to 12 days as compared to its alkyl chain analogs. Although both the fluorinated as well as non-fluorinated systems showed up to 90% release of curcumin in 12 days when incubated with lipase, a comparatively faster release was observed in the fluorinated polymers. Cell viability of HeLa cells up to 95% in aqueous solution of fluorinated polymers (100 μg/mL) demonstrated their excellent cyto-compatibility.