Are Microsoft 365 Emails Mysteriously Deleting Themselves? Here’s the Frustrating Reason Why

Why Are Outlook Emails Disappearing? Your Essential Step-by-Step Guide to Stop It.

An unsettling problem can affect Microsoft 365 users where important emails and contacts vanish from their accounts without warning. This issue appears to happen randomly, leaving both users and system administrators searching for answers. While not a new phenomenon, recent reports suggest that people are once again seeing their data disappear, causing significant disruption and concern. Understanding the potential causes is the first step toward protecting your information and resolving the problem if it happens to you.

This is not a simple glitch. Imagine watching emails delete themselves right before your eyes from your company account. This exact situation was reported by a user on a Microsoft support forum in August 2025. They explained that since the previous day, emails had been automatically disappearing. Despite multiple checks by several colleagues and the IT service department, no one could determine the root cause.

The affected person could initially recover some of the lost data. By logging directly into the Outlook web application, they could go to the “Deleted Items” folder and restore what was there. However, this only worked for emails deleted up to the morning of the previous day. All other messages remained permanently gone. This experience highlights the seriousness of the issue and the difficulty in finding a quick solution. The user’s account was part of a business, meaning the loss of data could have serious consequences for their work.

A Look at a Past Incident

This recent case is alarmingly similar to an event that occurred in early 2025. An administrator for a company using Microsoft 365 noticed a strange pattern. For a small number of users, all their contacts were being deleted every single day. There was no obvious pattern. The problem happened on computers running both Windows and macOS. The administrator checked the system logs and found a clue. The logs showed a huge number of “MovedToDeletedItems” actions being recorded for the affected mailboxes, but the source was unclear.

A well-known Microsoft expert suggested that an external client, such as a smartphone, might be causing this strange behavior and offered ideas for troubleshooting. The problem, however, escalated. A month later, the same administrator reported a new issue. A user suddenly found that emails were being deleted from their archive folder. Approximately 15,000 emails were gone, and the number of items in the folder was visibly shrinking. At the time, there was no clear explanation. Ideas included a full storage quota, but email rules were ruled out as a cause. The situation left the administrator and the user without a definite answer.

Common Things to Check First

When emails start disappearing, it is wise to first check for simple explanations. Misconfigured settings are often the culprit, and ruling them out can save you time and worry.

Check Your Outlook Rules

Outlook allows you to create rules that automatically manage incoming emails. For example, a rule could move all emails from a certain sender to a specific folder or to the trash. It is possible a rule was created by accident or that an existing rule is not working as intended. You should check your rules in the Outlook desktop application, the Outlook web version, and the mobile app, as rules can exist in different places and sometimes conflict.

Look at Your Storage Space

Every Microsoft 365 mailbox has a storage limit. If your mailbox is full, you may stop receiving new emails. While a full mailbox does not typically cause existing emails to be deleted, it can create other problems. It is good practice to check your storage usage and clean up old, unnecessary emails to ensure your account functions properly.

Review Retention Policies

In many companies, administrators set up retention policies. These are company-wide rules that can automatically delete emails and other items after a certain period. For example, a policy might delete everything in the “Deleted Items” folder after 30 days or remove emails older than seven years. While these are set by an administrator, it is worth asking your IT department if any such policies are active on your account.

Your Phone Could Be the Problem

If the simple checks do not solve the problem, the cause might be hiding on a device you use every day: your smartphone. Several reports from users who experienced disappearing emails pointed to the Outlook mobile app as the unexpected source of their troubles.

The issue often starts with the “Block Sender” feature. On your phone, you can block a contact or an email address to stop receiving junk mail. However, in some cases, users have accidentally blocked their own email address. When you block your own address, the Outlook app may interpret this as a command to treat all your own emails as spam. As a result, it starts automatically deleting them.

One user discovered that blocking their own email address as “spam” on their smartphone caused this exact behavior. An administrator dealing with a similar case reported that the only way they could fix the problem was to completely reset the user’s iPhone. After the reset, the email deletions stopped. If you are experiencing this issue, one of the most important steps you can take is to carefully check the blocked senders list within your Outlook mobile app.

Finding a Hidden Application with Advanced Tools

Sometimes, the problem is not with Outlook or your phone but with another application connected to your Microsoft 365 account. Many people use third-party apps for things like calendar scheduling, contact management, or email filtering. If one of these apps has a bug or a misconfigured setting, it can cause major problems.

For administrators, Microsoft provides a powerful tool called Microsoft Purview. Think of Purview as a detailed security log that records everything that happens in your Microsoft 365 environment. An administrator can use Purview to search for specific actions, like “MovedToDeletedItems” or soft deletes, which happen when an item is moved to the trash.

One administrator shared how they solved this problem. They used Purview to find the ClientAppId associated with the deletions. A ClientAppId is a unique code that identifies the exact application that performed an action. By looking up this ID, the administrator discovered that an email security application called Graphus was the culprit. A filter rule within that application was incorrectly set up and was deleting the user’s emails. Once the administrator removed the Graphus app’s permissions to access the user’s mailbox, the deletions stopped immediately. This shows that the root cause may lie outside of Microsoft’s own systems, in a connected service that was given access to the account.

Your Plan to Stop Emails from Deleting

If you are facing this issue, a systematic approach is the best way to find the cause and fix it. Here is a plan for both users and administrators.

For Users

• Start with the Basics: Immediately check your Outlook rules and your blocked senders list on all your devices, especially your phone.
• Check Deleted Items: Look in your “Deleted Items” folder and the “Recoverable Items” folder. You can often restore messages from there if you act quickly.
• Contact IT: If you cannot find the cause, report the problem to your IT department right away. Give them as much detail as possible, including when the problem started and what devices you use.

For Administrators

• Talk to the User: Ask the user about any new apps they have installed, new devices they have connected, or any settings they may have changed recently.
• Use Purview Audit Logs: The most powerful step is to run an audit log search in Microsoft Purview. Search for deletion activities in the user’s mailbox and look for the ClientAppId to identify the program making the changes.
• Investigate Third-Party Apps: Check the user’s Azure Active Directory account for any registered applications that have permission to access their mailbox. Pay close attention to any security or email filtering apps.
• Isolate the Problem: As a temporary test, you can disable mobile access for the user’s account. If the deletions stop, it strongly suggests the problem is with a mobile device. You can then work on the user’s phone to find the specific cause.

This problem of disappearing emails is stressful, but it is almost always solvable. The cause is rarely a major failure within Microsoft 365 itself. It is more often a misconfigured setting, a mobile app issue, or a conflict with a third-party application. By carefully checking each possibility, you can find the source of the trouble and secure your account.