Selfhosted
A place to share alternatives to popular online services that can be self-hosted without giving up privacy or locking you into a service you don't control.
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The alternative is to offer the Let's Encrypt bot access to your DNS service, typically in the form of an API token which you revoke after the bot verifies the domain. Access to the API is not needed for subsequent cert refreshes, only the first time.
The bot (or the proxy you use) needs to support the API of the DNS you use, naturally, but they support a wide variety of the most well-known ones.