Among the several possible uses of nanoparticulated systems in biomedicine, their potential as theragnostic agents has received significant interest in recent times. In this work, we have taken advantage of the medical applications of Gadolinium as a contrast agent with the versatility and huge array of possibilities that microfluidics can help to create doped Hydroxyapatite nanoparticles with magnetic properties in an efficient and functional way. First, with the help of Computational Fluid Dynamics (CFD), we performed a complete and precise study of all the elements and phases of our device to guarantee that our microfluidic system worked in the laminar regime and was not affected by the presence of nanoparticles through the flow requisite that is essential to guarantee homogeneous diffusion between the elements or phases in play. Then the obtained biomaterials were physiochemically characterized by means of XRD, FE-SEM, EDX, confocal Raman microscopy, and FT-IR, confirming the successful incorporation of the lanthanide element Gadolinium in part of the Ca (II) binding sites. Finally, the magnetic characterization confirmed the paramagnetic behaviour of the nanoparticles, demonstrating that, with a simple and automatized system, it is possible to obtain advanced nanomaterials that can offer a promising and innovative solution in theragnostic applications.