There has been an increasing and urgent demand to develop nucleic acid bioassays which not only offer high analytical performance but which are also amenable with point-of-care testing. Hydrogels present a versatile class of materials with biocompatible antifouling properties and the ability to be engineered for a range of advanced sensing applications. Fibrous substrates like nitrocellulose offer low-cost and durable platforms to run complex bioassays while enabling portability and ease of handling. We demonstrate herein the ability to synergistically combine these two materials into a portable biosensing platform by leveraging projection lithography. We demonstrate the direct polymerization of hydrogel sensing motifs within a range of fibrous substrates with precise control over their shape, size, location, and functionality. Spatial encoding of the hydrogel motifs enables the multiplex detection of multiple biomarkers on the same test. As a proof-of-concept, we apply the platform to the detection of microRNA, an emerging class of circulating biomarkers with promising potential for early diagnosis and monitoring of cancer. The assay offers a large dynamic range (over three orders of magnitude), high sensitivity (limit of detection of 2.5 amol), as well as versatility and ease of handling. Finally, the bioassay is validated using real biological samples, namely, total RNA extracted from the sera of late-stage breast cancer patients, demonstrating its utility and compatibility with clinical biosensing applications.