A Christian baker's lawsuit against the Colorado Civil Rights Commission alleging religious discrimination can proceed, a federal judge has ruled.

Masterpiece Cakeshop owner Jack Phillips' second suit against the agency alleges religious bias after he was punished for refusing to bake a cake celebrating a transgender reveal.

U.S. District Court Judge Wiley Y. Daniels ruled in a 53-page order on Friday that Phillips' suit can move forward.

It is the second time the baker has sued the commission, after the Supreme Court ruled in his favor in June over a discrimination claim when he was punished by the state for refusing to make a custom cake celebrating a homosexual wedding.

Masterpiece Cakeshop owner Jack Phillips' (above) second suit against the agency alleges religious bias against his shop by state regulators in a transgender cake case

Judge Daniels cited the Supreme Court's ruling in the first case in his order, noting that Justice Anthony Kennedy had written that the 'Commission's hostility was inconsistent with the First Amendment's guarantee that our laws be applied in a manner that is neutral toward religion.'

Daniels noted that Phillips had offered to sell other items to any customer regardless of sexual orientation, but declined to make custom cakes that conflicted with his Christian beliefs.

The judge wrote that Phillips 'declined to make cakes that 'demean LGBT people,' express racist views, celebrate Halloween, promote marijuana and alcohol, support Satan or satanic themes or beliefs, and, most famously, celebrate same-sex marriage.'

Judge Daniels also noted the Supreme Court's finding in the first case, that the Civil Rights Commission had no issue with other bakers who refused to make custom cakes displaying Biblical verses opposing homosexuality.

The second case stems from an incident that occurred on the day that the Supreme Court announced it would review the appeal in Phillips' first lawsuit.

Denver attorney Autumn Scardina, a transgender woman, made her way to Masterpiece Cakeshop in Lakewood, and requested a custom cake that was blue on the outside and pink on the inside.

Denver attorney Autumn Scardina (above), a transgender woman, spurred the second suit by requesting a cake that was blue outside and pink inside to celebrate transitioning

When Scardina informed Phillips that the cake was to celebrate her transition from male to female, he declined to make the cake but offered to sell Scardina other items, according to court filings.

Phillips' attorneys say in his suit that he 'believes as a matter of religious conviction that sex — the status of being male or female — is given by God, is biologically determined, is not determined by perceptions or feelings, and cannot be chosen or changed.'

The suit said that Phillips has been harassed and received death threats and that his small shop was vandalized while the wedding cake case made its way through the courts.

The Supreme Court's narrow ruling on Phillips' first case did not address whether a business can refuse service on religious grounds, and Colorado's Civil Rights Commission cracked down on the baker again over his stance on the transgender cake.

In the new lawsuit, Phillips alleges that Colorado violated his First Amendment right to practice his faith and 14th Amendment right to equal protection.

The suit seeks $100,000 in punitive damages from Aubrey Elenis, director of the Colorado Civil Rights Division. That claim was dismissed in Friday's order.

Judge Daniels in his ruling also dismissed outgoing Colorado Governor John Hickenlooper as a defendant, while finding that the other claims in the suit could proceed.