Email delivery issues are among the most common problems Microsoft 365 administrators face. Messages getting delayed, blocked, or never delivered can impact business operations immediately.
This guide explains how to troubleshoot mail flow issues in Exchange Online, using a clear, step-by-step approach that administrators can apply in real environments.
What Is Mail Flow in Exchange Online?
- Sender
mailbox or external mail server
- Exchange
Online Protection (EOP)
- Transport
rules and connectors
- Recipient
mailbox
Any issue at one of these stages can cause emails to be delayed, blocked, or rejected.
Common Exchange Online Mail Flow Issues
Administrators usually encounter mail flow problems such as:
- Emails
going to spam or quarantine
- External
emails not being delivered
- Internal
emails delayed
- Bounce-back
(NDR) messages
- Emails
blocked by spam filters
- Authentication
failures (SPF, DKIM, DMARC)
Understanding the type of issue is the first step
toward fixing it.
Step 1: Use Message Trace (Most Important Tool)
Message Trace is the primary tool for diagnosing mail
flow problems.
You can use it for:
- Track
the path of an email
- See
delivery status
- Identify
where the message was blocked or delayed
 |
| Message trace admin Center |
How to run a message trace:
- Go to Microsoft 365 Admin Center
- Open Exchange Admin Center
- Navigate
to Mail flow → Message trace
- You can Perform message trace based on sender, recipient, suject line and time range
- Review
results
Message trace provides detailed insight into what happened
to an email.
Step 2: Check the Delivery Status
Message trace results usually show one of these statuses:
- Delivered
– Message reached the mailbox
- Filtered
as spam – Blocked by spam filtering
- Quarantined
– Held for review
- Failed
– Delivery failed with error
- Pending
– Still being processed
If a message is marked as delivered but the user can’t see
it, check the Junk Email folder.
Step 3: Review Non-Delivery Reports (NDRs)
A Non-Delivery Report (NDR) is an automatic bounce
message that explains why delivery failed.
 |
| Delivery status notification |
Common NDR reasons include:
- Invalid
recipient address
- Domain
not found
- Sender
blocked
- Authentication
failure
- Mail blocked by mail flow rule
Always read the error code and description carefully.
Step 4: Check Spam and Malware Policies
Exchange Online Protection applies multiple filters to protect users.
Review:
- Anti-spam
policies
- Malware
policies
- Safe
sender lists
- Blocked
domains or IPs
Incorrect or overly strict policies are a frequent cause of
mail delivery problems.
Step 5: Verify Transport Rules (Mail Flow Rules)
Transport rules can:
- Block
messages
- Redirect
emails
- Modify
message headers
 |
| Eop-email-flow |
Check for rules that:
- Apply
to external senders
- Block
specific keywords
- Restrict
attachments or domains
Even one misconfigured rule can stop email delivery.
Step 6: Check Connectors (Hybrid or Third-Party)
If your organization uses:
- Hybrid
Exchange
- Third-party
email gateways
- External
relay servers
Then connectors must be reviewed.
 |
| Email-connector |
Verify:
- Connector
direction (inbound / outbound)
- TLS
requirements
- Sender
IP addresses
- Certificate
settings
Incorrect connector configuration often causes external
mail failures.
Step 7: Validate SPF, DKIM, and DMARC
Email authentication is critical for external mail delivery.
 |
| Email Authentication protocol |
What to check:
- SPF
record includes Microsoft 365
- DKIM
is enabled for your domain
- DMARC
policy is not overly strict
Authentication failures commonly cause emails to land in spam or get rejected.
Step 8: Check Quarantine
Sometimes emails are not blocked but quarantined.
Admins should:
- Review
quarantine regularly
- Release
false positives
- Adjust
policies if needed
Step 9: Review Mail Flow Reports
Mail flow reports provide a high-level overview of email activity.
 |
| Mail flow map |
These reports help identify:
- Spikes
in blocked messages
- External
sender issues
- Policy
effectiveness
Common Exchange Online Mail Flow Mistakes
Admins often make these mistakes:
- Ignoring
Message Trace
- Misconfiguring
spam policies
- Not
validating SPF/DKIM/DMARC
- Using
overly aggressive transport rules
- Forgetting
to check quarantine
Avoiding these saves hours of troubleshooting.
Best Practices for Exchange Online Mail Flow
Follow these best practices:
- Always
start with Message Trace
- Keep
spam policies balanced
- Test
transport rules carefully
- Monitor
mail flow reports
- Document
changes
Good documentation helps future troubleshooting.
Frequently Asked Questions (FAQ)
Why is email delivered but not visible?
It may be in Junk Email or quarantined.
How long does Message Trace data stay available?
Basic trace is available for 10 days, extended trace for 90
days.
Can mail flow issues affect internal mail?
Yes, especially if transport rules or connectors are
misconfigured.
Final Thoughts
Exchange Online provides powerful tools for troubleshooting
mail flow issues but knowing where to look and in what order makes all
the difference.
By following a structured approach—starting with Message Trace and ending with authentication checks—you can resolve most mail flow issues quickly and confidently.