Former pastor Jacob Malone was arrested on suspicion of raping a teenager in his congregation when his plane touched down in the US on Monday.

Malone, 33, was thought to be on the run but local police confirmed last week he was in Ecuador awaiting a return flight to hand himself in. The former pastor of Calvary Fellowship church in Exton, Pennsylvania, was taken into custody and is accused of rape, institutional sexual assault and other related charges according to The Philadelphia Enquirer.

The married pastor allegedly molested and impregnated a teenage girl in his church who had lived with his family after moving to the area.

The girl, who had known Malone and his family since the age of 12 while at his previous church in Arizona, moved with them aged 17. She was treated like an adopted daughter, according to one member of Calvary Fellowship.

The abuse began in late 2014, just months after she moved in, the girl told police. She claimed Malone gave her alcohol twice when she had turned 18, and that once when she was intoxicated, he molested her.

Malone resigned from his position in November 2015 after church leaders confronted him about the teen's pregnancy.

"Our church's goal in difficult moments like this is to protect the innocents, first of all," said Bill Bateman, pastor at Calvary Fellowship.

"And, number two, we strive to bring about repentance and restoration of the offender."