In a 75-page decision Judge Victor Marrero said he could not endorse "such a categorical and limitless assertion of presidential immunity from judicial process as being countenanced by the nation's constitutional plan."
Trump had argued he was immune from any criminal proceeding while in office. The judge said the president was entitled to no such "protective shield."
"The notion of federal supremacy and presidential immunity from judicial process that the president here invokes, unqualified and boundless in its reach as described above, cuts across the grain of these constitutional precedents," Marrero wrote.
The judge dismissed the president's lawsuit that was meant to stop the subpoena from being enforced.
President Trump's legal team filed an immediate notice of appeal to the 2nd US Circuit Court of Appeals, and the 2nd Circuit at least temporarily agreed to block the president's accounting firm from immediately having to hand over the requested tax returns in an emergency administrative stay Monday.
"Whether or not the Court ultimately agrees with the President's constitutional challenge to the subpoena, he is entitled to appellate review before his papers are forcibly disclosed to a state grand jury," the president's lawyer Patrick Strawbridge wrote.
The 2nd Circuit's order said the stay is granted "pending expedited review by a panel of the Court."
"We are very pleased that the U.S. Court of Appeals for the Second Circuit has issued a stay of the subpoena issued by New York County District Attorney Cy Vance," Trump lead counsel Jay Sekulow told ABC News.
Earlier Monday, in response to the judge's ruling that the president's tax returns are subject to subpoena, Trump took to Twitter to respond.
"The Radical Left Democrats have failed on all fronts, so now they are pushing local New York City and State Democrat prosecutors to go get President Trump," the president tweeted Monday morning. "A thing like this has never happened to any President before. Not even close!"
The Manhattan DA's office declined to comment to ABC News.
The subpoena was issued to Mazars USA, Trump's accounting firm, in August as part of an ongoing investigation into whether hush payments to Daniels and McDougal broke any state laws. The subpoena calls for financial and tax records of a number of entities and individuals, including those of President Trump.
The president's attorneys insisted "a sitting President of the United States is not subject to the criminal process while he is in office" and they filed a lawsuit to quash it.
"That doesn't immunize him permanently," the president's attorney William Consovoy said in the filing. "It means that while he is the commander in chief of our nation, 50 states can't decide that they are going to investigate the president while he tries to serve us as a country."
Manhattan District Attorney Cy Vance called that argument "remarkable" and said in September the lawsuit to block the taxes from subpoena should be dismissed.
"The law provides no such sweeping immunity," Assistant District Attorney Solomon Shinerock said in September. "They have no authority for the breathtaking grant of immunity that they seek."
The district attorney's office also accused the president of trying to run out the clock.
"Right now we're just in the very early stage of wanting to review materials," Shinerock said. "And this entire process I think is really designed by the plaintiff to make sure that doesn't happen."
ABC News' John Santucci contributed to this report.