The disclosed embodiments relate to a system that camouflages electromagnetic interference (EMI) fingerprints in EMI emissions from a computing system to enhance system security. During operation, the system monitors the EMI emissions from the computer system while the computer system is operating to produce corresponding EMI signals. Next, the system performs a Fast Fourier Transform (FFT) operation on the EMI signals. The system then converts an output of the FFT operation into a frequency-domain representation of the EMI signals. Next, the system generates a camouflaging signal based on the frequency-domain representation of the EMI signals. Finally, the system outputs the camouflaging signal through a transmitter to camouflage EMI fingerprints in the EMI emissions from the computer system.