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1. Configure Spam Filter Policy: First, users should verify ‘Advanced Spam Filter’ policies to check if an entire domain has been blocked. If yes, then all emails coming from that particular domain will go to Junk. Users can disable advanced spam filtering options that cause such problem. Users can also create ‘Safe Senders List’ in Office 365 to stop Office 365 email going to spam by going to Settings>> Options>> Block or Allow. Note that Exchange Online Protection (EOP) does not keep track of domains. It keeps only senders and recipients.
   

2. Using Directory Synchronization: This technique is applicable only to active staff and students. Usually, Office 365 email users are by default protected by Exchange Online Protection (EOP). In case of EOP-only subscribers, they can use director synchronization to fix this problem. Directory synchronization allows users to synchronize their own settings with EOP services. Thus EOP will have access to user’s ‘Safe Senders List’ and function accordingly.
   

3. Setting Connection Filter’s IP Allow list: To fix false negative issue of O365 emails to Junk, users can add senders’ IP addresses to IP allow list of connection filter. When users enable ‘Safe List Only’ option, they receive emails sent by the enlisted senders only to their inbox. In this case, adding IP address cannot eliminate the problem completely. As Office 365 email going to spam can’t be relinquish with IP.
   How to add an IP address to IP Allow list of Connection Filter

   • By extracting header of emails sent by preferred senders from Outlook or OWA.

   • By following the manual in ‘Use the EAC to change the default connection filter policy.

   • By manually finding IP address with Message Analyzer tab of Remote Connectivity. Analyzer. Users can also use CIP tag of X-Forefront-Antispam-Report header.
     

4. Verifying Junk Email Setting to stop internal emails going to Junk folder Office 365: Users can execute the below command to check the configuration setting of junk mail.Here,If TrustedListsOnly value is true, the setting is enabled.If ContactsTrusted value is true, user trusts both Contacts and Safe Senders.TrustedSendersAndDomains value shows contents of the user’s Safe Senders Lists.
   

5. Using Safe Senders List: Web Outlook users can use this method to stop emails from ending up in Junk folder. If there is a message with yellow colored safety tip, it means the email is in junk folder. Users can check the header of email whether it still contains SFV:SKN or SFV:NSPM stamp. It happens because Outlook ‘Safe Lists Only’ setting overrides the EOP setting. In case emails are going to junk folder irrespective of marking, turn off the option ‘Safe Lists Only.:
   

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Tip

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How can I stop Outlook or OWA putting incoming email into the Junk E-Mail folder?

1. Click on the Junk tool button in the toolbar near the top left of the Outlook window.

2. Click to select Junk E-Mail Options.
   

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3. Click the topmost option, labelled No Automatic Filtering.
   

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   (however, note that if you have specified any blocked senders, any messages from them will still go into the Junk E-Mail folder)

4. Click OK.

References
Learn to Stop Office 365 Emails Going to Junk Folder Permanently. https://www.office365computing.com/kb/office-365-email-going-to-spam.html

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