The disclosed embodiments relate to a system that camouflages 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 during operation of the computer system to produce corresponding EMI signals. Next, the system determines a dynamic amplitude of the EMI emissions based on the EMI signals. If the dynamic amplitude of the EMI emissions drops below a threshold value, the system executes synthetic transactions, which have interarrival times that, when superimposed on a workload of the computer system, cause the computer system to produce randomized EMI emissions.