The current era demands the development of well-designed point-of-care (POC) diagnostic systems capable of rapidly detecting multiple diseases. Nucleic Acid Test (NAT)-based detection has been extensively studied and optimized for high sensitivity and specificity. However, challenges remain in terms of operational ease, high costs, time constraints, and the requirement for skilled personnel. To address these limitations, there is an urgent need to integrate high-throughput techniques such as flow cytometry, mass spectrometry, and nuclear magnetic resonance (NMR) with lateral flow-based or biosensor-based platforms to develop simple, cost-effective, and rapid diagnostic systems for detecting multiple biomarkers. Flow cytometry employs lasers to identify the characteristics of cells, while MS ionizes and NMR magnetize the targeted biomolecules to identify specific characteristics and recognizes structures and interactions of different molecules. A critical step forward involves evaluating and integrating these methodologies, identifying technical gaps, and redesigning these systems into miniaturized, user-friendly versions suitable for POC applications. This chapter provides an in-depth analysis of these methodologies, highlighting key challenges and potential solutions for the advancement of next-generation diagnostic platforms. Research in this direction will enhance our understanding of these technologies and drive innovation toward more efficient and accessible diagnostic solutions.