re : ''the moment i delete the mail from the server it gets automatically deleted from my thunderbird account too'' This sounds like you have created an Imap mail account. There is a huge difference between Pop and Imap mail accounts. Imap mail accounts see a remote view of the folders on the server. Emails are stored on the server and you subscribe to remotely see those folders containing emails. The subscribed folders will connect with server and display whatever is on the server. So, basically, the folders you see in Thunderbird are one and the same as the folders on the server, which you can also access via webmail. When you delete an email via webmail or Thunderbird, you are deleting that email off the server. If you delete via webmail, then when Thunderbird connects to server, it will only show what is on server by synchronising the folder. some background info: When imap mail account connects with server, it downloads headers only and then retrieves the email when you select it, storing it in a temporary cache. You cannot read these emails if you are in 'offline' mode or lose internet connectivity. It does not store the email in Thunderbird. You can synchronise your subscribed folders for offline use to get a copy into Thunderbird profile folder. However, the folders are still synchronising with folders on server, so this aspect does not change. But, you can now read emails in offline mode. In Offline mode you can perform a backup of those emails. You can also copy emails into 'Local Folders', which means those emails will be stored in Thunderbird and those folders do not connect with server. Then when you are certain emails are properly in 'Local Folders'/you can read them - you can delete email in the imap mail account or directly via webmail, knowing you have a copy in 'Local Folders' mail account. re :''in outlook the mails got stored even if i deleted from the server'' I suspect that Outlook email client was using a POP mail account. POP mail accounts can only access the Inbox and download email to mail account inbox. The is no synchronising of folders. Usually, Pop mail accounts download and auto delete off server, but there are usually some settings to ask to 'Leave a copy of message on server'. This option is available in Thunderbird Account Settings. This means that if you delete via webmail, then that email will not get downloaded to Thunderbird or if already downloaded, it will only be deleted off server and not in Thunderbird. If you delete in Thunderbird, you can set settings to delete or not delete off server. Hope this explains what is going on. Some additional info that may help you. * https://support.mozilla.org/en-US/kb/imap-synchronization * http://kb.mozillazine.org/Profile_backup * http://kb.mozillazine.org/IMAP_backup