Fix One User Not Receiving Emails From External Organization in Exchange Online

Log into the Microsoft 365 Defender portal or the traditional Exchange admin center as an administrator.

Go to Mail flow > Message trace and click on 'Start a trace'.

Enter the external organization's domain in the Sender field and the affected user's email address in the Recipient field, set the time range to cover recent days, and click Search.

Review the delivery status (Delivered, Failed, Quarantined, or Filtered as Spam) to pinpoint the exact failure reason and which rule triggered it.

In the Exchange admin center, go to Recipients > Mailboxes, select the affected user, and verify that their mailbox has not exceeded its storage limit.

Instruct the user to open Outlook, navigate to their Junk Email folder to check for the missing emails, and ensure the external sender isn't accidentally listed in their Blocked Senders list.

Have the user go to Outlook Settings (gear icon) > Mail > Rules to ensure no custom rules are automatically deleting or moving emails from that specific external organization to another folder.

In the Exchange admin center, go to Mail flow > Rules. Review any rules that apply to external senders or inbound TLS connectors to ensure there are no exceptions dropping mail for this user.

Open the Microsoft 365 Defender portal, navigate to Email & Collaboration > Policies & Rules > Threat policies > Anti-spam, and check if quarantine policies are blocking the emails based on sender reputation.

If the message trace reveals no logs at all and the user's settings are correct, open a Microsoft support request from your Microsoft 365 admin center for deeper server-side investigation.