Downtown Church consists of cover songs, traditional songs, and original songs by Griffin, and Billboard has described the album as a "gospel-style record" influenced by traditional country music and blues. Griffin stated that the album was an attempt to familiarize pop fans with gospel music and that she intentionally used different styles to "mix it up". A Spanish hymn, "Virgen de Guadalupe", was suggested by Michael Ramos, a member of Griffin's band. Griffin stated that she had listened to Christian songs by Bob Dylan, but failed to connect to them, and wrote her songs partly in reaction to their certainty and her ambivalence about rigid doctrine. She told National Public Radio that she was "working through complicated feelings about religion" and recorded the album to explore them. Griffin described her original song "Coming Home to Me" as sharing a recurring theme of her music, loneliness and connection, and being about "what really goes on inside, deep down". The final song, "All Creatures of Our God and King" is based on Francis of Assisi.
The album was favorably reviewed by Slant Magazine reviewer Jonathan Keefe who praised Griffin as a natural fit for the songs and passionate "that even a nonbeliever can get on board". Jim Caligiuri of The Austin Chronicle called the album "haunting and original" and described the new direction compared to Griffin's previous album as a "gutsy move". Michael McCall of the Associated Press described the album as a "stunningly powerful and compassionate work". Kyle Matthews of the Associated Baptist Press noted that the album was cohesive despite a variety of styles and praised the song selection as "beyond stereotypes". Martin Bandyke of the Detroit Free Press called the album "uplifting and utterly majestic". Michael Corcora of the Austin American-Statesman praised Griffin as an "amazingly athletic singer" but criticized the album as "often divinely stirring" but lacking "a deep spiritual core". Noel Murray of The A.V. Club remarked on the choice of unconventional songs "I Smell A Rat", "Death's Got A Warrant", and "Virgen De Guadalupe" and described the album as "heartfelt", but "a little generic at times". Gage Henry of Paste stated that the album had "drastic turns" and praised Griffin's sentiment. Jewly Hight of American Songwriter praised the album and argued that the album had no "flat performances". David Belcher of the New York Times described the album as a "celebration" that was subtle but sometimes "foot-stomping". Jerry Shriver of USA Today praised the restraint and versatility of the album. Andrew Whitman of Christianity Today called the album "surprisingly diverse and beautifully sung" but argued that the secular "I Smell a Rat" did not fit with the religious material. Jay Lustig of The Star-Ledger described the album as "pop-folk-gospel fusion" and noted that the album includes songs that are slow, quick, mellow, and blunt. Mark Deming of Allmusic stated that Downtown Church was one of a string of good albums Griffin made since 1996 and was appealing "regardless of [one's] religious convictions".