"Only God knows God's miso soup". Is this a pun? In this chapter Buddha got cold, so Jesus tried to cook something for him. So he came up with a miso soup, and a joke. Or so it seems. But I don't understand this joke. "Only God knows God's miso soup". Is this a pun?
Yes, this is a Japanese pun. Unfortunately, this pun doesn't translate well to other languages.

The original phrases in Japanese are:



Image from buzz-manga.blog.jp


  神【かみ】のみぞ知る【しる】 (kami nomi zo shiru, only God knows)
  神【かみ】のみそ汁【しる】 (kami no miso shiru, God's miso soup)


Yes, both have the same reading: kaminomi[s/zo]shiru (except so and zo, which only differs by a voicing mark).

Also, the one that Jesus does in that scene is called dajare/oyaji gag, which usually employs the same reading for different meaning.