The disclosed embodiments provide a system that generates a reference EMI fingerprint to be used in detecting unwanted electronic components in a target asset. During operation, the system gathers reference EMI signals generated by a reference asset while the reference asset is executing a periodic workload, wherein the reference asset is of the same type as the target asset and is certified not to contain unwanted electronic components. Next, the system divides the reference EMI signals into a set of profiles, which comprise EMI signals for non-overlapping time intervals of a fixed size. The system then temporally aligns and merges profiles in the set of profiles to produce a reference profile. Next, the system generates the reference EMI fingerprint from the reference profile. Finally, the system compares a target EMI fingerprint for the target asset against the reference EMI fingerprint to determine whether the target asset contains unwanted electronic components.
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