The pair has taken up counselling sessions with Carl Lentz, a 38-year-old pastor at the church Bieber attends in New York, Hillsong.
According to celebrity magazines in the US, the two performers have been at odds over efforts by Bieber to seek reconciliation with ex-girlfriend Hailey Baldwin.
TMZ reported Bieber was reaching out to Baldwin as part of a new faith-driven "open and honest" approach to life, while People magazine quoted a source who said Gomez "wasn't thrilled" by the idea.
Bieber, who has become increasingly vocal about his Christian faith since he was baptised four years ago, shared on social media earlier this month how he believed Jesus was "changing" him.
Last month, Mr Lentz told US Weekly magazine he believed the 23-year-old Canadian has a "really deep, mature relationship with Jesus".