MSE is a security suite designed for consumers. It is based on the Forefront Client Security desktop agent, but solely provides malware detection and removal and lacks centralized management features. It includes the same anti-malware engine (dubbed "Microsoft Malware Protection Engine", or MSMPENG for short), and virus definitions that all other Microsoft desktop antimalware products share, including Forefront Client Security, Windows Live OneCare, and Windows Defender (Defender excludes the antivirus definitions which are separate from the antispyware definitions). Before installation, MSE checks for the validity of the installed copy of Microsoft Windows. MSE requires no registration or personal information. MSE will disable Windows Defender, as it provides protection against malware, not limited to spyware and adware.

Updates are published three times a day to Microsoft Update. Using default settings, archived files are decompressed, and then scanned. File downloads and e-mail attachments are also scanned. Its Dynamic Signature Service attempts to better identify malicious files by checking for updates if an application exhibits suspicious behavior. Before taking action against a suspect file, MSE prompts for user input. If no response is received in ten minutes, then the suspected malware is handled according to its default action, letting MSE determine what to do with the malware. System Restore points are created before removing found malware.