Joseph Scott Giaquinto, 35, was arrested on suspicion of several charges, including a crime motivated by bias, The Coloradoan reports.
Police had asked for the public's help in identifying the person who overturned benches, broke windows and threw a Bible into Islamic Center of Fort Collins, which is about 60 miles north of Denver.
A police spokeswoman told the newspaper that she did not have details on how police came to identify Giaquinto as the suspect.
The center's president, Tawfik Aboellail, said the man tried to break into the mosque about 4 am Sunday, but he did not get inside.
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The vandalism prompted the center to cancel religious classes for children that morning, but it has also led to an outpouring of support.
Many have also been making donations online to pay for repairs and improved security.
The Council on American-Islamic Relations had urged police to investigate the case as a possible hate crime. Police Chief John Hutto, who attended the support rally, said the incident has a "very real impact on our Muslim friends and neighbors."
"The criminal act against their sacred space is unacceptable," he said in a statement.