In this work, we present two types of microfluidic chips involving magnetic nanoparticles dispersed in cyclohexane with oleic acid. In the first case, the hydrophobically coated nanoparticles are self-assembled with an amphiphilic diblock copolymer by a double-emulsion process in order to prepare giant magnetic vesicles (polymersomes) in one step and at a high throughput. It was shown in literature that such diblock copolymer W/O/W emulsion droplets can evolve into polymersomes made of a thin (nanometric) magnetic membrane through a dewetting transition of the oil phase from the aqueous internal cores usually leading to “acorn-like” structures (polymer excess) sticking to the membranes. To address this issue and greatly speed up the process, the solvent removal by evaporation was replaced by a “shearing-off” of the vesicles in a simple PDMS chip designed to exert a balance between a magnetic gradient and viscous shear. In the second example, a simple oil-in-oil emulsion chip is used to obtain regular trains of magnetic droplets that circulate inside an inductor coil producing a radio-frequency magnetic field. We evidence that the heat produced by magnetic hyperthermia can be converted into a temperature rise even at the scale of nL droplets. The results are compared to heat transfer models in two limiting cases: adiabatic vs. dissipative. The aim is to decipher the delicate puzzle about the minimum size required for a tumor “phantom” to be heated by radio-frequency hyperthermia in a general scope of anticancer therapy.