It depends upon what you have set up. '''If you created a POP mail account:''' Pop accounts can only access the server Inbox and download new emails. By default servers assume you are downloading and storing emails on your computer, so server deletes emails off server when popped. However, there is a setting in Thunderbird which you can select to 'leave messages on server', so that when you pop download, a copy is still kept on server in Inbox. You can also set up additional settings eg: when I delete a message, delete it off server. All of these settings are chosen by you in this location: * Right click on pop mail account name in Folder Pane and select 'Settings' * Select 'Server Settings' for the pop mail account. See image below as guide. The pop account is totally independent of server. Folders do not synchronise. You can choose to download and keep emails on server. But, please note, pop accounts on server do have a quota and it may be less than an imap account because the server expects emails to be stored. From time to time you would need to check number of emails still on server and remove oldest/least valuable, empty the junk etc. If server reaches max quota, it may not be able to receive new emails. So bare this in mind. '''If you created an IMAP mail account:''' An imap mail account offers access to the emails stored on the server. You can subscribe to see folders. All folders synchronise with server folders of identical name. Imap account folders can only display what is contained in same folder on server. You can choose to download headers only or full copies. Check the 'Synchronisation & Storage' settings for imap account see example image below. More info: * https://support.mozilla.org/en-US/kb/imap-synchronization If you download full copies, it means you can read emails in offline mode and also perform your own backups of emails stored on the server, but it also uses more space on your computer. Whatever you do - move, copy, delete, mark as junk etc to a email in Thunderbird, then you will see the same occur on the server. The same is also true if you log on to webmail and delete emails off server, the next time Thunderbird imap account accesses server, it will show what is on server and so would appear to delete emails that you have already deleted off server. If you access server via another computer/phone and delete off server, then this will also show up as deleted in imap account in Thunderbird. So, do not assume the emails in an imap account are independent off the server. The folders are in effect one and the same. Basically, do not delete an email from an imap folder if you want to keep it on server. If you need to keep a copy of an email, but also need to remove emails off server to gain space/increase quota, then download full copy and get a copy put into the 'Local Folders' mail account as this will be independent of the server. Needless to say, whether you have a POP or IMAP account, backups are equally important.