Aaron Kenneth Hudgins of Timberlea was arrested and charged with one count each of possessing child pornography and accessing child pornography after Halifax police raided two locations on Friday morning.
The church announced his resignation Friday afternoon on their website.
"This morning we were made aware of the charges against Aaron Hudgins. We are deeply shocked and saddened by this news, and its impact on this community," the church wrote.
"Immediate action was taken, and Aaron has resigned from his position at Timberlea Baptist Church. Please be in prayer for the church, and his family."
Police started their investigation into allegations a man was in possession of child pornography last July.
On Friday police searched a residence on Sprucevale Drive in Timberlea and the National Research Council offices on Oxford Street in Halifax. They seized computer equipment during both searches.
Charles Drouin, spokesman for the National Research Council on Oxford Street, confirmed the office was searched, equipment was seized and an employee has been suspended without pay.
He was released from custody, but he can't communicate with children under the age of 18, possess a device able to connect to the internet and he must not be within 25 metres of a place frequented by children.
He's set to appear in Halifax Provincial Court on Dec.10.
Man's pastoral future up in the air
Peter Reid, executive director of the Atlantic Baptist Convention, called the news "tragic."
"I feel sick about it," he said.
The Baptist convention will not investigate the allegations itself. It can strip Hudgins of his pastoral duties, but didn't immediately.
"We have strict protocols around pastoral conduct. We don't sweep things like this under the rug," he said.
Reid said while they grant pastors their credentials and can remove them, the man's employment with the church is solely up to the leadership of the Timberlea Baptist Church.
It would be their call to remove him from the church or take him off the payroll.