Deploying Defender offline scan after malware detection

Published Jan 9, 2024 • Updated May 1, 2026

Overview

Microsoft Defender Offline (boot-level scan) helps remove persistent threats that resist normal cleaning. Use when layered detections suggest rootkit behavior or repeated reinfection.

When to choose offline scan vs reimage

  • Offline scan when time pressure is high, data must stay on disk, and IR approves.
  • Reimage when firmware/rootkit suspicion is high or regulatory policy mandates.

Procedure (Windows client)

  1. Ensure BitLocker recovery keys are escrowed and accessible.
  2. Schedule scan during maintenance window; warn user about long downtime.
  3. Launch Windows Security > Virus & threat protection > scan options > Microsoft Defender Offline scan—or deploy via scripted method per platform.
  4. After reboot and scan, review quarantine and threat history; run full scan again in Windows.

Follow-up

  • Patch exploited vulnerabilities.
  • Reset passwords for accounts that used the device.
  • Hunt for similar IOCs across tenant.

Documentation

Attach scan completion logs, threats removed, and any exclusions requested (with approvals).

Client communication template

“We ran a deep boot-level scan to remove malware that can hide from standard antivirus. The device is clean per current telemetry; we recommend password resets and will monitor for 48 hours.”

Related Articles

EDR deployment checklist for new workstations

## Overview Use this runbook when onboarding a new Windows workstation or re-imaging a device that...

security-endpoint-protection msp +1

Handling Defender for Business false positives

## Overview False positives waste analyst time and train users to ignore alerts. This article stand...

security-endpoint-protection msp +1

Application allowlisting with Windows Defender ASR rules

## Overview Attack Surface Reduction (ASR) rules reduce exploit surface by constraining Office macr...

security-endpoint-protection msp +1