The owner of Masterpiece Cakeshop in Lakewood is arguing that Colorado is violating his due-process rights.
The Alliance Defending Freedom said, "Colorado has done nothing to disavow or correct the Commission’s systemic and deep-seated opposition toward Phillips and his faith."
Phillips' first case based on his refusal to bake a wedding cake for a gay couple reached the Supreme Court this summer.
The Supreme Court ruled 7-2 in favor of Phillips. The justices' deliberations focused on the Colorado Civil Rights Commission's handling of the case and not, as many had expected, on the conflict between religious freedom and gay rights.
Phillips again sued the Colorado Civil Rights Commission and Gov. John Hickenlooper in August over another cake dispute.
The Alliance Defending Freedom said the suit stems from a June Civil Rights Commission ruling that cited Phillips for "probable cause" of discrimination based on "sex and or transgender status."
The 2017 commission complaint stated that Phillips refused to bake a cake celebrating a person's transition from male to female.
The district court has not yet heard that case.