Sample preparation and stabilization are critically important to downstream diagnostic assay sensitivity, as they directly impact the abundance and detection of analytes. Moreover, the Warfighter requires solutions for diagnostic sample processing that are simple, fast, and robust when operating in austere environments. Nanotraps® are hydrogel nanoparticles functionalized with chemical affinity baits that can capture low abundance proteins, peptides, metabolites, nucleic acids, small molecules, and whole virions, while also reducing high abundance interfering substances. Previously published studies have shown that Nanotraps can capture both virions and proteins from influenza virus, Rift Valley fever virus, HIV, and Venezuelan equine encephalitis virus (VEEV). Here, we applied Nanotrap® technology to Ebola virus (EBOV) diagnostic applications and found that Nanotrap® sample processing increased assay sensitivity for EBOV-specific nucleic acid tests and protein immunoassays in spiked human clinical matrices, and in matrices collected from nonhuman primate models of EBOV infection.