The amphipathic bioactive compounds curcumin, resveratrol, and mitomycin C, which have similar solubility parameter component distributions, have been studied for encapsulation under batch conditions into core-shell nanocarriers composed of external hydrophobically functionalized polyelectrolytes and an inner matrix of polyesters or polyester blends: poly(l-lactide), poly(lactide-co-glycolide), and/or poly(ethylene succinate). Our contribution comprises determining the influence of process parameters on the properties and quality of the final products, namely core-shell nanoparticles loaded with appropriate drugs, according to process analysis technologymanagement. The crucial roles of the organic phase dosing rates and process temperatures were carefully investigated. Moreover, a technically feasible method of removing organic solvents from aqueous dispersions─stripping with inert gas─was employed and evaluated via FT-IR studies. The experiments were supported by the calculation and analysis of solubility parameters (δ) and dispersion (δd), polar (δp), and hydrogen bond (δh) components utilizing HSPiP software. The payload locus and sample morphology were studied via atomic force microscopy and X-ray photoelectron spectroscopy analyses with Ar+ sputtering. It was demonstrated that dosing rates of organic phases not exceeding ca. 0.5 mL/min per 1 L of aqueous dispersion of hydrophobically functionalized polyelectrolytes made it possible to obtain core-shell nanoparticles of ca. 100-150 nm with a very narrow polydispersity (PdI < 0.2). The locus of amphipathic payloads in nanocarriers, mostly within the core polymeric structure, was in good agreement with the results of solubility parameter component studies: water-insoluble polyesters with both polar and nonpolar interactions between chains serve as good host materials for amphipathic drugs.