Thank you for reaching out to Atlassian Community!
Currently, there is no option to customize the Popular projects in the customer portal.
I've searched for the information about what makes it popular, but I found only for Jira Cloud where the popular depends on how many tickets the project has.
We have feature requests suggesting the implementation of the ability to change the order of the projects in the customer portal:
Please, click on vote and watch to receive updates about the feature.
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