There was a monastery, and the monks gave me a nice, warm place to sleep, and some soup.
Establishing Shot
The dark front entrance of the Monastery is some stock footage, not of an Irish church, but of the Cathedral Basilica of St. Louis in Missouri.
MAP
Interiors
The interiors of the monastery were initial planned for a real location, but due to the stunts needed for this sequence a set was built on a soundstage instead, according to the Agents of SHIELD Season One Declassified book.
Transitional Shot – Church Silhouette
The silhouette of the church, supposedly representing the Irish Monastery, is actually stock footage of a church in Prague, called St Vitus Cathedral.
MAP
(Agents of SHIELD S01E08, 2013)