Magnetic nanoparticles have been extensively explored as theranostic agents both in academic and clinical settings. Their self-assembly into nanohybrids using block copolymers can lead to new nanostructures with high functionalities and performances. Herein, we demonstrate a high-throughput and scalable method to elaborate magnetic micelles by the assembly of iron oxide magnetite nanoflowers, an efficient nanoheater, and the block copolymer Poly(styrene)-block-poly(acrylic acid) via a microfluidic-assisted nanoprecipitation method. We show that the size and shape of the magnetomicelles can be easily tuned by modulating the residence time in the microfluidic channel. In addition to their biocompatibility, we demonstrate the potential of these magnetic nanohybrids as multimodal theranostic platforms capable of generating heat by photothermia and functioning as negative contrast agents in magnetic resonance imaging and as imaging tracers in magnetic particle imaging. Notably, they outperform currently commercially available particles in terms of imaging functionalities.