i2pd_docs_en/docs/tutorials/yggdrasil-only-mode.md

Yggdrasil only router configuration

For a router talking to other routers and reseed servers through Yggdrasil only.
Start yggdrasil first and make sure you're running from a fresh i2pd installation. Create ~/.i2pd/i2pd.conf

daemon=true # note: remove it if you running on Windows!
ipv4=false
ipv6=false
ssu=false
ntcp2.enabled=false
ssu2.enabled=false
meshnets.yggdrasil=true  

If you use Yggdrasil subnet and want to bind your router to a particular address specify it with meshnets.yggaddress= your local yggdrasil address

Start i2pd, it will also reseed from an yggdrasil reseed server. No clearnet communication is involved.
Important: Make sure that the system clock is syncronized.