We have developed a next generation, miniaturized platform to diagnose disease at the point-of-care using diagnostic magnetic resonance (DMR-3). Utilizing a rapidly growing library of functionalized magnetic nanoparticles, DMR has previously been demonstrated as a versatile tool to quantitatively and rapidly detect disease biomarkers in unprocessed biological samples. A major hurdle for bringing DMR to the point-of-care has been its sensitivity to temperature variation. As an alternative to costly and bulky mechanisms to control temperature, we have implemented an automated feedback system to track and compensate for the temperature drift, which enables reliable and robust DMR measurements in realistic clinical environments (4-50 °C). Furthermore, the new system interfaces with a mobile device to facilitate system control and data sharing over wireless networks. With such features, the DMR-3 platform can function as a self-contained laboratory even in resource-limited, remote settings. The clinical potential of the new system is demonstrated by detecting trace amounts of proteins and as few as 10 bacteria (Staphylococcus aureus) in a short time frame (<30 min).