The church, which defines itself as Evangelical Lutheran, still has 7 million members.
Last year, however, 54,000 people decided to drop out. During the same time frame, the national church also attracted more than 7,500 new members.
There are differences in the drop-off rate between the towns and smaller communities.
"That community has a high attendance at church services," the local pastor Michael Brodin told the TT news agency, before underlining that the congregation was small.
"They have a tradition of piety."
The church itself has noted the urban rural divide.
"Most people in Stockholm have moved here, which means they don't have their childhood church nearby," Jonas Bromander, head of analysis at the Church of Sweden's national office.
"It means the relationship is weakened."
Half of Stockholm and Gothenburg residents are now members, while less than half of Malmö's residents are members.