BI agents arrived in black SUVs at the six-bedroom, 4,800sqft holiday home in Rehoboth Beach, Delaware, which the US president bought for $2.7m in 2017.
It was the third search in three months after agents had previously scoured his main home in Wilmington, Delaware, and also a private office.
Mr Biden, who was in Washington, knew about the beach house search in advance and gave his consent, meaning the FBI did not need a warrant.
No documents with classified markings were found – but agents took away some of Mr Biden’s handwritten notes, and other items, “for review”.
Bob Bauer, Mr Biden’s personal lawyer, said: “They took for further review some materials and handwritten notes that appear to relate to his time as vice-president.”
Mr Bauer said the US president had offered the US department of justice and the FBI his “full support and co-operation”, and the search was “planned” rather than being a raid.
Merrick Garland, the US attorney general, has already appointed special counsel Robert Hur to investigate the handling of classified material by Mr Biden and his staff when he left the office of vice-president in 2017.
Mr Hur is looking into why dozens of documents were not handed over to the US national archives, which is required by federal law.
The latest FBI search happened on the same day that Mr Hur officially began overseeing the investigation.
Jonathan Turley, a law professor at George Washington University Law School, said: “The White House is in a freefall. Any knowledge... is going to show intent to retain those documents. This is a very serious question.”
The latest search was yet another setback for Mr Biden as he prepared to launch his re-election campaign following his State of the Union address which is set for February 7.
Mr Biden had previously condemned his predecessor, Donald Trump, as “irresponsible” after classified documents were found at his Mar-a-Lago home in Florida.
The controversy over Mr Biden’s own papers began on November 2 when classified documents were found at an office he had used at a think-tank’s premises in Washington, after he ceased to be vice-president in 2017.
One of Mr Biden’s lawyers had found the material and informed the FBI, who then searched the office.
Then, on January 20, the FBI spent 13 hours searching the president’s home in Wilmington. Classified documents had been stored there in his garage next to his Corvette car, and in his personal library.
It is illegal to knowingly remove or retain classified material after leaving office. There was no comment from the FBI or the DoJ.
The US national archives has reportedly now asked that all former presidents and vice-presidents should conduct searches of their personal records.