The first bomb went off outside Calvary Baptist Church (pictured above) in the area of Las Cruces on Sunday morning, inside a nearby mailbox.
The second detonated twenty minutes later inside a bin outside Holy Cross Catholic Church (pictured below), four miles away in the same district, while worshippers were celebrating Mass.
The explosion caused the stained glass of the church to smash. No one was injured in either of the two blasts.
Fr John Anderson, the priest of Holy Cross, told The Las Cruces Sun News: "I was right in the middle of saying the words 'take and eat, this is my body' and there was a Pow! I mean, I knew it had to be more than a gunshot.
"I didn't know if it was a shotgun blast, I didn't know what. But it was very loud and I just kept on saying the words."
No one has claimed responsibility for the attacks, which police believe to be related.
Dan Trujillo, from Las Cruces police force, told the Daily Telegraph: "Just the fact that they were at churches the same day a half an hour apart or so, that leads us to believe it could be something related.
"We can't tell them what to do, but we can tell them to be on the lookout for anything suspicious.
"Don't go poking around in trash cans or mailboxes. If you have any suspicion of anything that's out of the ordinary, please call to police and leave it up to the officers to look it over."