Point-of-care diagnostic devices aid in the early and rapid detection of immunological markers leading to better medical outcomes. Lateral flow immunoassays (LFIA) are fast assays that provide both qualitative and semi-quantitative results on site. Sample preparation for LFIA tests is usually done manually with multiple mixing steps and is prone to errors. The iQuant Auto is an entirely automated system that can handle sample preparation, effective transfer to lateral flow test membrane, and subsequent result estimation. The system uses a pneumatic system for fluid handling and sample preparation, and an image-based fluorescence reader for reaction visualization. The device works with test specific milli-fluidic lateral flow kit called iQPrep Kit, which has integrated reagent storage areas and valves for fluid control. The test kit can be manufactured using standard manufacturing techniques and can be produced at scale cheaply. The iQPrep Kit can be modified to test for various markers like HbA1c, Vitamin D, and TSH, while the hardware for sample preparation and the fluorescence reader remains the same. The device has a minimalist and intelligible graphical interface aiding smooth operation by less skilled people at resource-limited settings. Standard reference cartridges of different volume ratios were used to validate the functionality of the instrument. The intra- instrument coefficient of variation (CoV) of the mobile kit reader was found to be less than 0.62%. The positional accuracy of the system to ensure precise kit engagement with the other auxiliary systems was checked, and the CoV was 0.16%. The fluid handling capabilities were tested, and it was found that an average fluid loss of 10 µl results due to the liquid adherence to fluid channel walls and valve interfaces. The iQuant Auto is an easily operable, total analysis system for immunodiagnostics.