Police announced on Tuesday that they had arrested Muhammad Syed, 51, as the "primary suspect" in the killings in Albuquerque, New Mexico.
Officials, civil rights groups and the media had stoked fears in the Islamic community of bias attacks against Muslims.
President Joe Biden had tweeted that he was "angered" by the killings and that his "administration stands strongly with the Muslim community".
The nationality of Syed has not been disclosed by officials, but the possibility of anti-Shia killings in the US could indicate that the religious turmoil in Pakistan and Afghanistan where Sunni terrorist groups target Shias has reached the US.
Two of the killings took place during the observances of Muharram, a period of religious mourning for Shias.
The Council on American-Islamic Relations (CAIR) admitted on Tuesday that "anti-Shia hatred" may have "motivated the killings" after its Deputy Director Edward Ahmed Mitchell had earlier issued a general warning that "the lives of Albuquerque Muslims are in danger" and asked Muslims across the US to "exercise vigilance".
CAIR National Executive Director Nihad Awad said: "Although we are waiting to learn more about these crimes, we are disturbed by early indications that the alleged killer may have been targeting particular members of the Shia community."
Alburquerque police said they found evidence that the alleged killer knew the victims and "an interpersonal conflict may have led to the shootings".
They said that bullet casings found at the site of the shooting of two Pakistanis, Aftab Hussein on July 26 and Muhammad Afzaal Hussain on August 1, matched a gun at Syed's residence and they filed charges against him.
Albuquerque Police Chief Harold Medina said police were working with prosecutors on "potential charges" in the other two cases -- Mohammad Zaheer Ahmadi, an Afghan who was killed in November, and Naeem Hussain, a Pakistani, on August 5.
The police said that as detectives prepared to search Syed's home on Monday, he drove out in a Volkswagen (ETR: VOWG_p ) Jetta that was used in at least one of the killings.
The detectives detained Syed and searched his home and the vehicle and found more evidence that tied him to the killings, police said.
(Arul Louis can be contacted at email@example.com and followed at @arulouis)
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