Backing up an Office 365 mailbox can become complicated when the account contains years of emails, attachments, contacts, calendars, and other mailbox data. A simple export may also become difficult when only specific folders or date ranges need to be preserved.

For a controlled backup, I would first identify whether the requirement is for the complete mailbox or only selected folders. The SysInfo Office 365 Backup Tool allows users to preview the mailbox hierarchy and select the required folders before starting the backup. This is useful when there is no need to download the entire Microsoft 365 mailbox.

Another useful approach is applying a Date Filter when the backup only needs emails from a particular period. The tool also provides an option to exclude duplicate items, which can help prevent unnecessary copies from being included in the resulting backup.

The backup can be saved in formats such as PST, PDF, EML, MSG, MBOX, CSV, and other supported formats depending on the intended use. For users who need to work with Outlook later, PST can be selected as the destination format.

For organizations, the Assign Impersonation option can also be useful when multiple Office 365 mailboxes need to be processed with the appropriate administrator permissions. This avoids handling every mailbox as a completely separate manual task.

My preferred workflow would be to preview the mailbox, select the necessary folders, apply a date range if required, enable duplicate exclusion, choose the required output format, and then start the backup.

A reliable way to backup Office 365 mailbox data without losing the folder structure is to use a dedicated Office 365 backup tool. SysTools Office 365 Backup Tool can export mailbox data while maintaining the original folder hierarchy, including Inbox, Sent Items, Drafts, custom folders, and subfolders. It supports backing up emails along with attachments and other mailbox data in formats such as PST, EML, MSG, and PDF. You can also apply date filters or select specific folders when required. For organizations managing multiple Microsoft 365 mailboxes, the tool provides a convenient way to perform bulk backups without manually exporting each mailbox. This makes it easier to preserve the original organization of mailbox data and access the backup whenever needed.