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Accurate, rapid, and low-cost molecular diagnostics is essential in managing outbreaks of infectious diseases, such as the pandemic of coronavirus disease (COVID-19). Accordingly, microfluidic paper-based analytical devices (μPADs) have emerged as promising diagnostic tools. Among the extensive efforts to improve the performance and usability of μPADs, electrochemical impedance spectroscopy (EIS) based sensing mechanisms have shown great promise, because of their high sensitivity and label-free operations. However, the method to improve EIS biosensing on μPADs is less explored. Here, we present an experimental approach to enhancing the biosensing performance of paper-based EIS nanobiosensors with working electrodes (WEs) decorated with vertically grown zinc oxide nanowires (ZnO NWs). Through a comparison among different EIS settings and an examination of ZnO-WE effects on EIS measurements, we show that Faradaic processes with Fe-based electron mediators are more reliable for ZnO-NW-enhanced working electrodes. We calibrate sensors featuring varied morphologies of ZnO NWs and achieve a low limit of detection (0.4 pg ml−1) for detecting p24 antigen as a marker for human immunodeficiency virus (HIV). Through theoretical analysis, imaging, and electrochemical characterizations, we reveal that the total surface area and electrochemical surface area indicate the sensitivity and sensing range of the EIS nanobiosensors. Finally, we demonstrate that the nanobiosensors are capable of differentiating the concentrations (blank, 10 ng ml−1, 100 ng ml−1, and 1 μg ml−1) of IgG antibody (CR3022) to SARS-CoV-2 in human serum samples, thus confirming the feasibility of applying the devices to COVID-19 diagnosis. This work provides a methodology that can inform the rational design of high-performance EIS-based μPADs and has the potential to facilitate rapid diagnosis in pandemics., Highlights • Paper-based impedance biosensors can provide accurate, rapid, and low-cost diagnostics of infectious diseases. • Nanowires can be directly synthesized on paper-based electrodes for biosensing in a facile process. • Electrochemical surface areas of nanowires affect the sensitivity and detection range of impedance-based biosensors. • Testing of a protein marker specific to COVID-19 has been demonstrated.