We present synthetic strategies for the utilization of functionalized polyester nanoparticles that enable efficient chemistries to conjugate targeting units and dendritic molecular transporter entities to form potent carrier systems for targeted drug delivery and transport across biological barriers. Polyester nanoparticles that feature functionalities such as keto, amine and allyl groups to react with moieties present in bioactive compounds, could be prepared in a one-pot procedure that improves the prior-developed drop-in cross-linking method. Integrated keto functionalities were utilized with amines of the N-terminus of peptide targeting units in high yielding reductive amination reactions. Thiol-ene reaction conditions were developed to perform mild addition reactions with targeting units, such as a novel c-RGD, but also cell penetrating dendritic transporter structures. The synthesis of targeting peptide–nanoparticle conjugates (NP–P–dye), dendritic molecular transporter nanoparticle conjugates (NP–MT–dye) as well as conjugates that contained both bioactive entities (NP–P–MT–dye), could be achieved. To study these systems in vitro, imaging units such as Alexa Fluor® 594 were introduced as another additional component to label primarily the nanoparticle backbone. This work describes several efficient post-modification strategies to accommodate the demands of biomaterials for mild conjugation chemistries utilizing amine and thiol units to form polyester bioconjugates with specific functionalities as a platform for an array of therapeutic applications.