Dowd's resignation comes a few days after President Trump hired the outspoken lawyer Joseph E. diGenova, who claimed a group of Federal Bureau of Investigation and Department of Justice people were trying to frame Trump, without providing any evidence.
With Dowd gone, Trump's outside team has three lawyers: Ty Cobb, Jay Sekulow, and Joseph diGenova.
Dowd is said to have believed that such a meeting between Trump, known to speak off the cuff and take himself down rabbit holes, and Mueller's team was not in the president's best interests.
Trump's latest tariffs are a response to allegations that China steals USA technologies through legal requirements slapped on American businesses who want to sell their products to China.
The departure of attorney John Dowd removes the primary negotiator and legal strategist who had been moulding Trump's defence.
But the president has been impatient for Mr Mueller's investigation to come to a close, and the loss of Mr Dowd may only drag out the process.
Mr DiGenova has advocated a much more confrontational approach, including the idea for Deputy Attorney General Rod Rosenstein, who oversees Mr Mueller's work, to be removed and appointed as a judge. "If you shut down or throttle the Mueller investigation. you will plunge this country into a constitutional crisis".
Some of his allies have urged him to be more aggressive in dealing with the special counsel's office.
Earlier today, Trump attacked former vice president Joe Biden are in a row over which of them would prevail in an imaginary brawl.
As part of that, Mueller is also investigating Trump for possible obstruction of justice, and his team of investigators has been in talks on arranging an interview with the president.
The days of applauding Mueller, however, may soon be over, as the Special Counsel appears to have left the question of Russian collusion behind in favor of the question of whether President Trump obstructed justice when he fired former FBI Director James Comey.