The queen and her husband, Prince Philip, met with survivors and former British soldiers who were among those who liberated the camp where teenage diarist Anne Frank and her sister Margot died 70 years ago.
"I'm very happy that the queen can do this for the British soldiers," said Rudi Oppenheimer, one of the Bergen-Belsen survivors who greeted the queen at the site in northern Germany, near Celle.
"They did so much. They never talked about it, they couldn't talk about it. They didn't tell their wives or their children, they were so horrified by what they saw. All the corpses," said Oppenheimer, who immigrated to Britain after the war.
Both the queen, 89, and Philip, 94, supported the British war effort against the Nazis during World War II.
The queen, then a princess, was moved out of Buckingham Palace at the height of the blitz for safety's sake, retreating to Windsor. She later served in the Women's Auxiliary Territorial Service and was trained as both a military truck driver and a mechanic. Prince Philip served throughout the war in the Royal Navy.
The queen and Philip made state visits to Germany in May 1965, May 1978, October 1992 and November 2004, but this was the first time they visited the site of a former Nazi camp.
"The memory of the Holocaust remains such a fundamental aspect of modern Jewish identity that the queen's journey to memorialize the victims will be viewed as tremendously significant by Jewish communities across the world," said Ephraim Mirvis, the chief rabbi of the United Hebrew Congregations of the Commonwealth in Britain, who met with the queen at the Bergen-Belsen ceremony.
The queen and Philip were shown through parts of the former camp by the memorial's director. They paused at a special memorial for Frank and her sister, who was born the same year as Elizabeth, before walking alone along a long path to the House of Silence, a modern structure set up as a place of reflection for visitors. The two then placed a wreath at a memorial to the camp's victims.
They shook hands and talked with survivors, liberators and schoolchildren on hand to greet them.
Oppenheimer, who was only 12 at the time Bergen-Belsen was liberated but still remembers the vivid images of naked corpses piled high around the camp, said it was a great honor for him to be invited to the ceremony.
"For me it's wonderful," said Oppenheimer, 83, who speaks on behalf of the Holocaust Educational Trust and talked to the AP ahead of the queen's visit. "But it upsets me that neither of my parents know about it, or my uncle, he was always so proud that we are integrated into the English system. Imagine his little Rudi shaking hands with the queen."
Earlier in the day in Berlin, a more festive atmosphere prevailed as flag-waving crowds greeted Elizabeth next to Berlin's landmark Brandenburg Gate.
Elizabeth, looking upbeat and spry despite a busy schedule, was handed bouquets by schoolchildren who waited outside her hotel and she smiled broadly when greeted by a little boy dressed like a king, complete with a blue and gold crown.
The reception was similar to the one Elizabeth has received since arriving in Berlin Tuesday night, with large crowds greeting her at all stops and German media providing blanket coverage of the visit. She was due to return home later Friday.