Chikungunya is a mosquito-borne infectious disease, which causes acute fever and joint pain, and can trigger long term arthritis. In the present study, we demonstrate a label-free detection of chikungunya virus non-structural protein 3 (CHIKV-nsP3), which is responsible for alphavirus replication, using electrochemical impedance spectroscopy (EIS). This is hitherto, the first work addressing the detection of CHIKV-nsP3 using biosensors. The immunosensors were developed by modifying a gold surface using self-assembled monolayer of 11-mercaptoundecanoic acid and 6-mercaptohexanol. Anti-CHIKV-nsP3 antibodies were attached to the sensor surface via cabodiimide coupling reaction. The impedance spectra were fit to an equivalent circuit, and the percentage change in charge transfer resistance was correlated to the antigen concentration, and a linear working range from 25 ng/ml to 1 μg/ml of CHIKV-nsP3 was obtained. The limit of detection was 8 ng/ml and the limit of quantification was 17 ng/ml. The biosensor was also found to be highly specific to CHIKV-nsP3. The sensor was further tested for matrix effect from human serum, and appreciable recoveries ranging from 97% to 106% was observed. The results illustrate the potential of EIS based immunosensors with CHIKV-nsP3 as a suitable biomarker for direct and sensitive detection of chikungunya. © The Author(s) 2019.