The power couple toured the historic home hours after she performed at the Ziggo Dome.
A message on the Anne Frank House Facebook.com page reads: "American singer Beyonce and rapper & producer Jay Z visited the Anne Frank House today. They were more than an hour inside and very impressed by their visit to the hiding place of Anne Frank."
Before leaving the home, Beyonce wrote a message in the guestbook and posed for photographs.
Her tour of the house, where the Jewish teenager hid from the Nazis during World War Two, was a lot less newsworthy than Justin Bieber's visit last year (13) - he sparked controversy when he wrote that he hoped the writer "would have been a belieber" in the guest book.
His comment sparked outrage among other tourists, with many pouring scorn on his message in subsequent notes in the visitors book, and it prompted a frenzy of criticism on social networking websites.
Museum bosses had to step in to back Bieber and thank him for visiting the house.
Spokeswoman Annemarie Bekker said, "He's a 19-year-old boy taking the effort to come and see the museum, and we'd like to point that out, and I think it's quite innocent what he put down."
Another representative, Maatje Mostart, tells the Bbc, "He's 19. It's a crazy life he's living, he didn't mean bad (sic)... and also it's nice that he made the effort, he didn't have to come."
Anne Frank died at the age of 15 at the Bergen-Belsen concentration camp in Germany in 1945. She became one of the best-known Jewish victims of the Holocaust following the publication of her diary in 1947.