Thanks to Courtney Stein for bringing up the topic, and to Valerie Hunter and Holly Huckabe for contributing to this list! I appreciate that our conversations can turn into such an interesting blog post and an excellent form of procrastination.
What We Lost, originally published as Once Was Lost by Sara Zarr
The story of a pastor's daughter who has lost her faith after her mother is sent to rehab and a local girl goes missing.
Pure by Terra Elan McVoy
Five friends wear purity rings and promise to stay "pure" until marriage, until one breaks her promise. This book looks at how their friendship changes, and how the girls define purity.
Purity by Jackson Pearce
This book is about purity rings as well, but less about faith than Pure is. I still think that it is an interesting one to check out, though!
Small Town Sinners by Melissa Walker
Walker looks at Hell Houses in this book, and the struggle one girl feels about her faith and role in her church. It's an excellent book, and very well-researched.
The Opposite of Hallelujah by Anna Jarzab
When Caro's sister Hannah returns home after spending ten years in a convent as a nun, Caro must reconcile with past secrets, current relationships, and her own faith.
The Girl of Fire and Thorns by Rae Carson (and sequels The Crown of Embers and The Bitter Kingdom)
In this fantasy trilogy, Princess Elisa is the carrier of the godstone and is destined for a great service to God. I love that Carson has created a psuedo-Christian religion in this trilogy to help explore Elisa's faith in a god, other people, and in herself.
Queen of Secrets by Jenny Meyerhoff
This is a modern day retelling of the Biblical story of Esther.
What Would Emma Do? by Eileen Cook
Emma grows up in an ultra-religious town and she can't wait to get out, but if she reveals what she knows about the hypocrites in her town, she may just be burning her one-way ticket out.
The Miseducation of Cameron Post by emily m. danforth
All These Things I've Done by Gabrielle Zevin (and sequels Because It Is My Blood and In the Age of Love and Chocolate)
This futuristic trilogy is about a self-professed good Catholic girl from a crime family who must walk a fine line between morality and legality to protect her family.
Taken by Storm by Angela Morrison (and sequels Unbroken Connection and Cayman Summer)
This trilogy is about Leesie and how she balances her loyalty to her family and Mormon faith with the love she feels for Michael, a boy with his own scars and demons.
Keep Sweet by Michele Dominguez Greene and The Chosen One by Carol Lynch Williams
These two books I grouped together because they are about girls who are trapped in religious cults and are forced into arranged marriages or witness abuse. They're fascinating and horrifying, but very different from each other.
Can you think of any other books that have to do with faith in YA? (Or even middle grade...Holly suggested The Higher Power of Lucky, which I totally second.)
ETA: Reader suggestions from the comments! (Unless I indicate otherwise, I have not read these.)
Grave Mercy & His Fair Assassin trilogy by Robin LaFevers
DragonKeeper Chronicles by Donita K. Paul
Because of Winn Dixie by Kate DiCamillo
Under the Mermaid Angel by Martha Moore
Are You There God? It's Me Margaret by Judy Blume
Stealing Parker by Miranda Kenneally
Burned by Ellen Hopkins (I've read this one, I would put it sort of near examples of extreme religious behavior.)