Note: This guide explains how to use a preliminary feature. Don’t expect all the flows to be fully build out, yet.
The setup and management of additional organizations works in a similar way as setting up the first organization: It requires logging in as the admin-user. The admin login link has the form of https://your-installation.gitpod.cloud/api/login/ots/admin/<token>, where the token part is compared with a hash of the token stored in a Secret named admin-credentials in the default namespace of the Gitpod installation. It has a data entry named admin.json, which is filled with a JSON shape of the form: 
{
    "tokenHash": "someHash",        # the hashed token value
    "algo" "someHashAlgorithm",     # default: "sha512"
    "expiresAt": 123124             # int64 unix timestamp after which this token is considered expired
}
We don’t have a common way to manipulate this from the outside, yet. Here is the Go code that Gitpod uses internally.
Instructions on how to build the previewctl tool in the gitpod-io/gitpod repository: 
cd dev/preview/previewctl
go build .
./previewctl admin credentials create

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Log in to the Gitpod installation

After following the link, you should be seeing the Gitpod dashboard, as the admin-user.

Logged in as admin-user - Gitpod Dashboard

Also note how the Organization dropdown at the top left now shows:
  1. All organizations there are on this installation (admin-user is made member of all of them on every login)
  2. The “Create Organization” button
As the Secret is mounted via kubernetes, it make take some time until the content is reflected in the pod that handles the login request. If you experience an “token expired” message, please wait a bit and try again.

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Create an additional Organization

After clicking “Create Organization”, choose a name, confirm and the new organization is created.

Create another organization - Create Organization View

For other people to join that organization, SSO has to be configured next.

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Configuring SSO

This can be done under “Organization Settings” -> “SSO” and works as described in Configure SSO.

Setup SSO for that other organization - Setup SSO View

The current process has the limitation that the person who configures SSO also needs to be able to sign-up with it (in order to verify it).
After the SSO config is verified and activated, logout (as admin-user).

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Login to any organization

To login as regular user again, go to https://your-installation.gitpod.cloud/login, select an organization to log in to by providing the organization name and select “Continue with SSO”.

Login to any organization - Login View

To pre-select an organization to log in with, so users only have to hit “Continue with SSO”, append the search parameter ?orgSlug=<orgName> to any URL. This works for for workspace creation URLs as well, e.g. https://your-installation.gitpod.cloud/?orgSlug=supercorp#https://github.com/some/repo