The most performing techniques enabling early diagnosis of infectious diseases rely on nucleic acid detection. Today, because of their high technicality and cost, nucleic acid amplification tests (NAAT) are of benefit only to a small fraction of the population of developing countries. By reducing costs, paper microfluidics has the potential to considerably facilitate the accessibility to NAAT. So far, studies about NAATs on paper have used model samples and most often fresh reagents. In real situations, reagents must be stored and detrimental interactions may occur between clinical samples, reagents and paper that unavoidably degrade the performances of the test. This, coupled to the fact that a number of constraints have not been taken into account (limited settings, transportation in tough conditions…) prevents the conclusions of past studies to be transferrable to the field or to the point-of-care where they are the most needed. This letter brings microfluidic paper NAATs much closer to the field, by using clinical samples and operating in a resource-limited setting. We first performed isothermal reverse transcription and Recombinase Polymerase Amplification (RT-RPA) of synthetic Ribonucleic Acid (RNA) of Ebola virus using paper microfluidics devices. We further applied this method in Guinea to detect the presence of Ebola virus in human sample RNA extracts, with minimal facilities (carry-on detection device and freeze-dried reagents on paper). RT-RPA results were available in few minutes and demonstrate a sensitivity of 85.3% compared to the gold-standard RT-PCR on a set of 50 patient samples. Furthermore, the realization of a nine-spot multilayered device achieving the parallel detection of three distinct RNA sequences opens a route toward the detection of multiple viral strains or pathogens.