Herein, we present the large-scale fabrication of multiplexed three-electrode sensors used in a point-of-care device platform that couples a magnetic bead-based immunoassay strategy with amperometric detection for rapid and highly sensitive analysis. The multiplexed sensors consisted of eight independent electrochemical cells, each with a carbon nanotube (CNT) working electrode, CNT counter electrode and a silver-silver chloride quasi-reference electrode. The microchips were fabricated on flexible polyethylene terephthalate (PET) sheets by sequential multilayer inkjet printing (IJP) of silver, CNT and insulator inks that were either simultaneously or subsequently post-processed (e.g. through UV photo-polymerization or photonic curing). Finally, plastic wells were mounted on top of the inkjet-printed patterns to obtain an eight-well microtiter plate where each well had a solution capacity of 50 μL. Due to the high precision of the IJP process, the microtiter plates showed high reproducibility among the individual electrochemical cells (1–2% of deviation). Furthermore, the microchips can be reusable for at least up to 20 times as demonstrated herein. In a customized multichannel potentiostat with eight implemented magnets matching the positions of the working electrodes, the electrochemical readout of magnetic bead based sandwich and competitive immunoassays was successfully realized for the detection of thyroid-stimulating hormone (TSH) and atrazine (ATR) in aqueous and urine samples, respectively. The achieved limits of detection for ATR (i.e. 0.01 μg/L) and TSH (i.e. 0.5 μIU/mL) demonstrated the potential of the IJP microtiter plates for the environmental and biological quantification of analytes in a very reliable high throughput platform. This work shows that IJP has certainly reached the status of a batch production tool for electroanalytical sensing platforms