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@Asmus Koefoed Welcome to the Atlassian community
You cannot change the colors through the delivered application. There is this app in the marketplace but I am not sure it has what you are after. https://marketplace.atlassian.com/apps/1212632/look-and-feel-for-bitbucket-server?tab=overview&hosting=datacenter
@Asmus Koefoed You could change the theme. This still does not give you access to change individual colors but it does provide you with the ability to have a different look and feel.
Go to your repository’s admin-tab, and click “Appearance Settings” under “Additional options/settings”.
Here you can choose from a list of themes, and when switching theme in the dropdown the preview to the right will update immediately.