Send & Receive Issues

Fix Internal Microsoft 365 Email Going to Junk Folder

Maira Mehtab Sep 29, 2026 868 views

Question details

Internal emails from a colleague in the same domain are being routed to the Junk folder, bypassing the Safe Senders list.

Why Internal Microsoft 365 Email Goes to Junk

Product: Microsoft 365
Device & OS: not provided
Scenario: Receiving important communications from an internal employee within the same organization.
Observed behavior: Messages are consistently delivered to the Junk Email folder even after the sender has been unblocked and added to the user's Safe Senders list.

Before you start

Verify that you do not have any local inbox rules set up in your email client that might be automatically moving messages from this specific sender to the Junk folder.

Solution 1Recommended

Investigate via Microsoft 365 Defender Quarantine and Trace

This solution requires a Microsoft 365 administrator to review security triggers, message trace logs, and spam confidence levels that override individual user settings.

Microsoft 365 security policies take precedence over local user settings. Even if a sender is on a Safe Senders list, tenant-level filters will quarantine or junk emails if they exhibit suspicious behavior, contain phishing indicators, or score a high spam confidence level (SCL).

Access Microsoft 365 Defender

Navigate to Quarantine

Go to 'Email & collaboration' in the left-hand menu, click on 'Review', and select 'Quarantine' to check if the internal emails are being flagged by anti-spam policies.

Run a Message Trace

Use the Message Trace tool in the Exchange admin center to track the affected emails. Look specifically at the Spam Confidence Level (SCL) assigned to the messages.

Check Tenant-Level Filters

Review your organization's mail-flow rules and anti-spam policies to ensure no overly aggressive filters are catching internal domain traffic.

Investigate via Microsoft 365 Defender Quarantine and Trace

Compromised Account Warning: If an internal account consistently triggers high SCL scores or malware alerts, it may be compromised. Administrators should immediately audit the account for suspicious login activity.

Solution 2

Clear Conflicting Local Outlook Rules

Check for and remove any hidden or conflicting rules within the Outlook desktop client that might be overriding safe sender configurations.

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Frequently Asked Questions

What is a Spam Confidence Level (SCL) in Microsoft 365?

The Spam Confidence Level (SCL) is a rating assigned by Exchange Online Protection to incoming emails. A higher score indicates a higher probability that the email is spam, which can cause even internal messages to be sent to the Junk folder.

Why does Microsoft Defender ignore my Safe Senders list?

Tenant-wide security configurations, such as anti-phishing policies or malware protections set by administrators, take precedence over an individual user's Safe Senders list to protect the organization from potentially compromised internal accounts.

Can mail-flow rules cause emails to go to the Junk folder?

Yes. Exchange administrators can create mail-flow (transport) rules that bypass standard spam filtering to intentionally route certain emails to Junk, based on specific keywords, attachments, or sender patterns.

Outlook & Email Problems