It’ll delete the metadata from the Git branch first before eventually making those changes to the org.
In the Deploy Options tab, there are now extra Deploy Types available for Git Orgs: "Destructive" and "Standard & Destructive". Select any of these options will allow you to choose components to be deleted from Git.
The deployment type options are available for both work items and regular deployments.
For Deployments, after selecting components to be deleted from Git, you can commit the changes to the feature branch and create a pull request to merge them to the main branch.