Using compact desktop NMR systems for rapid characterization of relaxation properties directly after synthesis can expedite the development of functional magnetic nanoparticles. Therefore, an automated system that combines a miniaturized NMR relaxometer and a flow-based microreactor for online synthesis and characterization of magnetic iron oxide nanoparticles is constructed and tested. NMR relaxation properties are quantified online with a 0.5 T permanent magnet for measurement of transverse ( T2) and longitudinal ( T1) relaxation times. Nanoparticles with a primary particle size of about 25 nm are prepared by coprecipitation in a tape-based microreactor that utilizes 3D hydrodynamic flow focusing to avoid channel clogging. Cluster sizes are expeditiously optimized for maximum transverse relaxivity of 115.5 mM s-1. The compact process control system is an efficient tool that speeds up synthesis optimization and product characterization of magnetic nanoparticles for nanomedical, theranostic, and NMR-based biosensing applications.