He engaged in a gun battle which left one police officer and two civilians dead but ultimately surrendered inside the building after a five-hour siege.
The full extent of casualties was murky in the immediate aftermath of the gunman's capture.
A police spokeswoman, Lieutenant Catherine Buckley, initially said she had no confirmation of fatalities, adding that police were still searching for possible victims who might have been left behind in the clinic as the building was evacuated.
State Attorney General Cynthia Coffman posted a message on her official Twitter account a short time later saying two people had been killed, but that post was quickly deleted and replaced with another lamenting a "tragic loss of life."
The Colorado Springs chapter of the Fraternal Order of Police, a law enforcement union, then reported on its Twitter page that one police officer had died.
Buckley put the number of people taken to area hospitals at 11, including five officers, but it was not immediately clear whether that tally included the fatality reported by the police union.
A Reuters photographer at the scene saw a man in a white T-shirt, with his hands cuffed behind his back, being taken out of an armored police vehicle and placed in an unmarked squad car. Authorities said they did not know the suspect's identity but believed he acted alone.
"We did get officers inside the building. They were able to shout to the suspect and make communication with him and at that point they were able to get him to surrender and he was taken into custody," Buckley said.
An hour earlier, police said progress in securing the building was slowed by the fact that the gunman brought "some bags" with him into the clinic and left several items outside, all of which needed to be checked for possible booby traps or explosives.
After the arrest, Buckley said it would take hours more, and perhaps days, for investigators to fully process the crime scene.
Police swarmed the area around the building after an emergency call reporting shots fired at about 11.30am local time (6.30pm GMT), and officers ultimately confronted the suspect inside the building, Buckley said.
Television footage aired by CNN showed a number of clinic staff and patients being escorted safely into police vehicles from the building, which lies on the northwest side of Colorado Springs, about 70 miles south of Denver.
The FBI and agents from the US Bureau of Alcohol, Tobacco, Firearms and Explosives were assisting local law enforcement investigators.
President Barack Obama was notified of the shooting by his Homeland Security adviser, Lisa Monaco, and "will be updated on the situation as necessary, a White House official said.
The Planned Parenthood center provides abortions, screening for sexually transmitted diseases, pregnancy testing and other services, according to its website.
"We don't yet know the full circumstances and motives behind this criminal action," Vicki Cowart, president and CEO of Planned Parenthood Rocky Mountains, said in a statement .