Pecker, 72, said he signed an agreement with Trump's personal lawyer Michael Cohen to assign the rights to former Playboy model Karen McDougal's story to a shell company that would hide the fact that Trump was paying for it.
He said he called off the deal after speaking with a company lawyer.
"Michael Cohen said, 'The boss is going to be very angry with you.' And I said, 'I'm sorry, I'm not going forward, the deal is off,'" Pecker testified.
"He was very angry, very upset, screaming, basically, at me," Pecker said of Cohen.
Donald Trump has pleaded not guilty to 34 felony counts and denied an affair with Stormy Daniels. (EPA PHOTO)
Pecker is a key witness in the case against the former US president, who is accused of falsifying business records to cover up a hush-money payment to another woman who said she had a sexual encounter with Trump, porn star Stormy Daniels.
Pecker testified that he told Cohen that Daniels was looking to sell her story in the weeks before the November 2016 election.
He said he was frustrated that the Enquirer's parent company, American Media, had already paid thousands of dollars to bury other stories that were unflattering to Trump.
"I thought it should come off the market, and if anyone was going to buy it, Michael Cohen and Donald Trump should buy it," Pecker said.
Pecker said Cohen pressed American Media to buy Daniels' story but Pecker testified he did not want to be involved with a porn star.
Prosecutors say Pecker, who has not been charged with a crime, engaged in a conspiracy with Trump and Cohen to corrupt the 2016 election by suppressing unflattering stories that might hurt Trump's candidacy.
Pecker testified that after McDougal told his editor that she had a year-long affair with Trump in 2006 and 2007, he advised Trump to buy her silence.
Pecker said he told Cohen he did not want the Enquirer to pay for the story, as it had already paid $US30,000 ($A46,000) to buy the silence of a Trump Tower doorman who claimed Trump had fathered a child of out wedlock, which turned out not to be true.
He said American Media paid McDougal after Cohen promised Trump would reimburse the company.
Pecker said Cohen set up a shell company to disguise any payment from Trump's company, before Pecker backed out of the deal.
McDougal's story about the affair was never published - a practice known as "catch and kill" that is considered unethical by mainstream journalism outlets.
Nevertheless, the Wall Street Journal published a story four days before the election revealing that American Media had bought McDougal's story.
"Donald Trump was very upset, saying, 'How could this happen, I thought you had this under control," Pecker testified.
McDougal is expected to testify later in the trial.
Cohen is also expected to be a prominent witness.
He has said he arranged a $US130,000 payment to Daniels to keep quiet about a liaison she says she had with Trump in 2006.
Prosecutors say Trump illegally falsified business records by disguising his reimbursement payments to Cohen as legal fees.
Trump has pleaded not guilty to 34 felony counts and denied having sex with Daniels, whose real name is Stephanie Clifford.
He has also denied having an affair with McDougal.
Hush money payments themselves are not illegal, and Trump's lawyers have argued the Daniels payout was personal and unrelated to his campaign.
Prosecutors say the payment was a campaign expense that should have been disclosed, and that Trump's arrangement with the Enquirer deceived voters by suppressing stories of alleged extramarital affairs at a time when he faced accusations of sexual misbehaviour.
