Donald and Melania Trump have laid stones and flowers at a memorial to the 11 people killed in the Pittsburgh shooting, as thousands of protestors gathered to oppose the visit and accuse him for "stoking hatred".
The president and First Lady were accompanied by Rabbi Jeffrey Myers, who led them on Tuesday to the makeshift memorials erected to the eight men and three women killed by a gunman who stormed into the shul during Saturday's Shabbat service and opened fire.
The shooter reportedly shouted "all these Jews have to die".
The president was joined by his daughter Ivanka Trump, who converted to Judaism on her marriage to Jared Kushner, who also attended.
White House spokesperson Sarah Sanders told reporters: "The president was very moved by the visit and his time with the rabbi and called it very humbling and sad."
But Mr Trump's visit prompted anger from those who accused him of stoking hatred. An estimated 4,000 people protested in the city's Squirrel Hill neighbourhood, as he paid his respects.
One protestor carried a sign saying Mr Trump should "apologize for stoking hatred or go home" and another carried one saying: "You know who else was a nationalist? Hitler"
One speaker told the crowd: "Your words and your policies have emboldened the white nationalist movement."
It was organised by Bend the Arc, a group of progressive Jews who previously wrote an open letter urging the president not to visit.