However federal police said that when arrested the suspects claimed that the first blazes were set as "a joke" and that other churches were set alight to throw investigators off the track.
Governor Bob Riley said the fires did not appear to be "any type of conspiracy against organised religion" or the Baptist faith.
Benjamin Nathan Moseley and Russell Lee Debusk, both 19-year-old students at Birmingham-Southern College, appeared in federal court and were ordered held on church arson charges pending a hearing on Friday.
Matthew Lee Cloyd, a 20-year-old junior at the University of Alabama at Birmingham, was also arrested over the fires.
The fires broke out at five Baptist churches in Bibb County, south of Birmingham, on February 3 and four Baptist churches in west Alabama on February 7.
The fires were mostly set at night in the sanctuary near the altar when the buildings were empty.
The federal Alcohol, Tobacco, Firearms and Explosives agency had made the investigation its top priority, with scores of federal agents joining state and local officers.
Acquaintances of the accused said DeBusk and Moseley were both amateur actors who were known as pranksters.
They performed in campus plays and appeared in a documentary film.
Moseley confessed to the arsons after his arrest, investigators alleged in documents presented to the court.
The documents said Moseley allegedly told agents that he, Cloyd and Debusk went to Bibb County in Cloyd's sport utility vehicle on February 2 and set fire to five churches.
A witness quoted Cloyd as allegedly saying Moseley did it "as a joke and it got out of hand".
Moseley also allegedly told agents the four fires in west Alabama were set "as a diversion to throw investigators off," an attempt that "obviously did not work."
During the investigation police said that there appeared to be no racial pattern in the fires; four were white congregations, five were black.
All were Baptist churches, the dominant faith in the region, but agents were uncertain if that denomination was a factor.
The three students are white and all either attend or previously were enrolled at Birmingham-Southern, a liberal arts college affiliated with the Methodist church.