There are a few references in the film to God and to organised religion. Although for the most part Python treats religion quite well in this film, there are times when they seem to be poking fun at the organised aspects of Christianity. For instance, there’s the scene showing the monks in procession through the village streets. “Pie Jesu Domine, Dona eis requiem.” Their chants are interspersed with a flogging to the head, administered by planks which they are carrying. This scene no doubt makes fun of the Christian practice of self-flagellation which dates back to the ancient Church. The belief was that through abuse against ones self, one could make penance for the sins which one committed.

Also attached to Christianity, and religion in general, is a feeling by many people that there are too many rules and “thou shalt not’s” that you must follow in order to be a member. This is made light of in the scene where Arthur asks the monks for the Holy hand grenade. Very specific directions on how to use it are read from the “Book of Armaments.” Also represented is the tendency of lay people to get those directions wrong.

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ARTHUR: Consult the Book of Armaments!
MAYNARD: Armaments, Chapter Two, Verses Nine to Twenty-One.
BROTHER: "And Saint Attila raised the hand grenade up on high, saying, 'Oh, Lord, bless this thy hand grenade that with it thou mayest blow thy enemies to tiny bits, in thy mercy.' And the Lord did grin, and people did feast upon the lambs, and sloths, and carp, and anchovies, and orangutans, and breakfast cereals, and fruit bats, and large --"
MAYNARD: Skip a bit, Brother.
BROTHER: "And the Lord spake, saying, 'First shalt thou take out the Holy Pin. Then, shalt thou count to three, no more, no less. Three shalt be the number thou shalt count, and the number of the counting shalt be three. Four shalt thou not count, nor either count thou two, excepting that thou then proceed to three. Five is right out. Once the number three, being the third number, be reached, then lobbest thou thy Holy Hand Grenade of Antioch towards thou foe, who being naughty in my sight, shall snuff it.'"
MAYNARD: Amen.
ALL: Amen.
ARTHUR: Right! One... two... five!
???: Three, sir!
ARTHUR: Three! [boom]

God is also represented in an interesting light. He is depicted, true to medieval views, as being above the people, in a lofty cloud, passing judgement. God does not seem to appreciate the customs adopted by the church.

GOD: Arthur! Arthur, King of the Britons! Oh, don't grovel! If there's one thing I can't stand, it's people groveling.
ARTHUR: Sorry--
GOD: And don't apologize. Every time I try to talk to someone it's "sorry this" and "forgive me that" and "I'm not worthy". What are you doing now!?
ARTHUR: I'm averting my eyes, oh Lord.
GOD: Well, don't. It's like those miserable Psalms -- they're so depressing. Now knock it off!
ARTHUR: Yes, Lord.
GOD: Right! Arthur, King of the Britons -- you're Knights of the Round Table shall have a task to make them an example in these dark times.
ARTHUR: Good idea, oh Lord!
GOD: 'Course it's a good idea! Behold! Arthur, this is the Holy Grail. Look well, Arthur, for it is your sacred task to seek this Grail. That is your purpose, Arthur -- the Quest for the Holy Grail.
ARTHUR: A blessing!
LAUNCELOT: A blessing from the Lord!
GALAHAD: God be praised!

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