Conjugated polymer nanoparticles (CPNs) are a promising class of nanomaterials for biomedical applications, such as bioimaging, gene and drug delivery/release, photodynamic therapy (PDT), photothermal therapy (PTT), and environmental sensing. Over the past decade, many reports have been published detailing their synthesis and their various potential applications, including some very comprehensive reviews of these topics. In contrast, there is a distinct lack of overview of the role the stabilizing copolymer shells have on the properties of CPNs. This review attempts to correct this oversight by scrutinizing reports detailing the synthesis and application of CPNs stabilized with some commonly-used copolymers, namely F127 (Pluronic poly(ethylene glycol)-block-poly(propylene glycol)-block-poly(ethylene glycol) diacrylate), PSMA (poly(styrene-co-maleic anhydride)), PLGA (poly(D, L-lactide-co-glycolide)) and PEG (polyethylene glycol) derivatives. The analysis of the reported physicochemical properties and biological applications of these CPNs provides insights into the advantages of each group of copolymers for specific applications and offers a set of guidance criteria for the selection of an appropriate copolymer when designing CPNs-based probes. Finally, the challenges and outlooks in the field are highlighted.