Most likely causes are a rule, blocked sender entry, junk setting, or a device/app moving mail before Outlook on Windows shows it.
Try this in order:
- Check Outlook rules in Classic Outlook
- In Outlook, go to Home > Rules > Manage Rules & Alerts.
- Look for any rule that deletes messages, moves messages to Deleted Items, or moves mail based on broad conditions.
- Disable or delete suspicious rules.
- Check Junk E-mail settings in Classic Outlook
- Go to Home > Junk > Junk E-mail Options.
- On the Options tab, make sure Permanently delete suspected junk e-mail instead of moving it to the Junk E-mail folder is cleared.
- This setting can cause mail judged as junk to bypass Junk E-mail and go straight to deletion.
- Risk: if this option is enabled, false positives are harder to recover because they do not stay in Junk.
- Review the junk filter level
- In the same Junk E-mail Options window, check the protection level.
- Higher protection catches more junk, but it also increases the chance that legitimate mail is treated as junk.
- If this started after tightening spam settings, reduce the protection level.
- Check blocked and safe sender lists
- In Outlook on the web, go to Settings > Mail > Junk email.
- Remove legitimate senders or domains from Blocked senders.
- Add trusted senders or domains under Safe senders and domains.
- Messages from addresses or domains on the safe senders list should not be moved to Junk.
- Check web rules and sweep settings
- In Outlook on the web, review Settings > Mail > Rules.
- Remove rules that delete messages, move them to Deleted Items, or broadly process incoming mail.
- Also check Sweep settings and remove suspicious entries.
- Check ignored conversations
- Open Deleted Items.
- Select a message from a thread that keeps getting deleted.
- On the Home tab, if Ignore is highlighted, select it and choose Stop Ignoring Conversation.
- Check other devices or mail apps
- If a phone or tablet is connected to the mailbox, it may be moving mail.
- A known case is Samsung’s default mail app: entries in Spam addresses can cause new messages to move to Junk or Unwanted.
- On the Samsung device, open the mail app, then Settings > General Settings > Spam addresses, and remove entries that should not be there.
If the mailbox was recently compromised, hidden rules or blocked entries may still be active even after changing the password. In that case, checking Outlook on the web is especially important because some rules are easier to find there.