When I use a profile and customize a pinned repository, it is pinned to my profile, but I need to pin it to my organization.
How do I pin it to my organization?
On GitHub.com, navigate to the main page of the repository. In the top-right corner of the page, click Star. Optionally, to unstar a previously starred repository, click Unstar.
You can use organizations for free, with GitHub Free, which includes limited features on private repositories.
AFAIK, it should be done from your Organization account, not from your personal account.
Update
Steps for Enterprise GitHub, but I assume the user experience would be same for public GitHub.
Assuming you are the administrator for your organization, when you open profile page, you see your personal profile page.
On the left side, you see your profile picture, description, user name, etc. You might see an "Add Bio" as well.
Below that you see list of organizations (icons only) you are part of, including the one for which you are admin.
Now click on the Organization icon to open the organization profile.
By default, it opens up the Repositories Tab.
Below the tabs, on the far right, you would see a link to "Customize Pinned Repositories". From here, you can choose up to six public repositories to showcase on your organization page.
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