The implementation of multiplexed point-of-care biosensors is a top priority to address the current epidemic problems originated by widespread pathogenic infections, like those caused by viruses or bacteria. A rapid and accurate detection, identification, and quantification of the infectious pathogens is essential not only to facilitate a prompt treatment but also to prevent onward transmission, reduce economic expenses, and significantly promote healthcare in resource-constrained environments. We have developed a nanoplasmonic biosensor based on nanohole arrays for fast and highly sensitive analysis in a simple and direct configuration. Our microarray is integrated into a microfluidic system to allow for highthroughput detection of multiple targets in a few minutes, without the need of sample pretreatment or amplification steps. Previously, we demonstrated the utility of the biosensor for the detection of hazardous live viruses, such as the Ebola or Vaccinia viruses, measured directly in biological media. Most recently we proved the truly multiplexing capability of our plasmonic microarray with the simultaneous identification and quantification of Chlamydia trachomatis and Neisseria gonorrhoeae in urine samples. We are able to detect and distinguish the two different bacteria with detection limits in the range of 102 -103 bacteria/mL. With recent advances in plasmonics, optimized surface chemistry, and microfluidics integration, our biosensors could provide a non-invasive and rapid diagnosis at the point of care, especially when we combine the detection on a compact and low-cost optical reader.