Hi Akshay,
By 'pop up', do you mean the new mail desktop alert banner? By default, new mail alert is turned on for emails delivered to Inbox. If you have rules which moved emails to subfolders, the new mail alert doesn't work for these emails ended up in subfolders.
In this case, you will have to modify the rules to include the "Display a desktop alert" action.

Besides, please also go to File > Options > Mail, under “Message arrival” heading, make sure the "Display a Desktop Alert" option is enabled.

Regards,
Steve Fan
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