Bioinspired recombinant polypeptides represent a highly promising tool in biomedical research, being protein intrinsic constituents of both cells and their natural matrices. In this regard, a very interesting model is represented by polypeptides inspired by elastin, which naturally confers rubber-like elasticity to tissues, and is able to undergo wide deformations without rupture. In this paper, a microparticle system based on a recombinant human elastin-like polypeptide (HELP) is reported for drug delivery applications. HELP microparticles are prepared through a water-in-oil emulsion of an aqueous solution of recombinant polypeptide in isoctane, followed by enzymatic cross-linking. Superparamagnetic iron oxide nanoparticles are introduced in this system with the purpose of conferring magnetic properties to the microspheres, and thus controlling their targeting and tracking as drug vectors. The obtained microparticles are characterized in terms of morphology, structure, magnetic properties, drug release, and magnetic drivability, showing interesting and promising results for further biomedical applications.