The disclosed computer-implemented method for managing security programs may include (i) identifying a security program configured to analyze files on a client device to detect malicious files, (ii) determining a result the security program would report for an analysis of a file on the client device, (iii) intercepting an attempt by the security program to analyze the file, and (iv) determining, based on the result the security program would report for the analysis of the file, whether to permit the security program to analyze the file. Various other methods, systems, and computer-readable media are also disclosed.