The dreadful incident claimed at least 11 lives and wounded scores more including two police officers, police said.
The first attack took place at the Santa Maria Roman Catholic Church in Surabaya, killing four people, including one or more bombers, AP quoted a police official as saying.
Minutes later another explosion struck the Christian Church of Diponegoro while the third hit the city's Pantekosta Church, the police official added.
President Joko Jokowi Widodo rushed to Surabaya in the aftermath of the attacks while Indonesia's Foreign Minister Retno Marsudi took to Twitter to express her grief over the incident.
"Deepest condolences to the victims and families of the bombing victims in Surabaya. #UnitedAgainstTerrorism#WeAreNotAfraid," she tweeted.
The bombings were carried out by at least five suicide bombers, including a veiled woman having two children with her, a senior police official told on condition of anonymity.
A witness described the woman with children, saying she was carrying two bags at the Diponegoro church.
"I was frightened... many people were screaming," a 23-year-old eyewitness told AFP after the blast.
Indonesia has been on high alert following the attacks by homegrown terrorists, while some accused the ISIS group of the same. So far no one has claimed responsibility for the bombings during Sunday services.
However, the police have closed off all three locations as they are working to identify the victims. The attackers are yet to be identified.
"These attacks on peaceful worshipers are an affront to the tolerance and diversity embraced by Indonesians. The United States stands with the people of Indonesia, and we offer our deepest condolences to the families of the victims," the statement read.
Indonesia, the most populous Muslim-majority country, has witnessed a number of attacks, claimed by Islamist militancy in recent past.
The 2002 attack is considered to be the worst-ever bombing in the history of Indonesia, which killed 202 people outside a bar and nightclub in Bali. Following the bombing, the authorities launched a crackdown on extremist groups.