Magnetite nanoparticles (MNPs) represent one of the most intensively studied types of iron oxide nanoparticles in various fields, including biomedicine, pharmaceutics, bioengineering, and industry. Since their properties in terms of size, shape, and surface charge significantly affects their efficiency towards the envisaged application, it is fundamentally important to develop a new synthesis route that allows for the control and modulation of the nanoparticle features. In this context, the aim of the present study was to develop a new method for the synthesis of MNPs. Specifically, a microfluidic lab-on-chip (LoC) device was used to obtain MNPs with controlled properties. The study investigated the influence of iron precursor solution concentration and flowed onto the final properties of the nanomaterials. The synthesized MNPs were characterized in terms of size, morphology, structure, composition, and stability. Results proved the formation of magnetite as a single mineral phase. Moreover, the uniform spherical shape and narrow size distribution were demonstrated. Optimal characteristics regarding MNPs crystallinity, uniformity, and thermal stability were obtained at higher concentrations and lower flows. In this manner, the potential of the LoC device is a promising tool for the synthesis of nanomaterials by ensuring the necessary uniformity for all final applications.