Paul Pelosi was attacked and severely beaten by an assailant with a hammer after he had broken into their home on Friday morning. Mr Pelosi, 82, suffered blunt force injuries to his head and body.
The assailant specifically targeted the home, authorities said. The suspect was later identified by San Francisco Police Department as 42-year-old David Depape.
He will be charged with attempted homicide, assault with a deadly weapon, elder abuse, burglary and several additional felonies, the police department said.
The US President condemned the attack and drew parallels with the US Capitol riots.
Speaking at an event in Philadelphia on Friday evening, he said he had spoken to Mrs Pelosi who said her husband was in "good spirits".
He went on to address reports that the assailant had repeated the "same chant" heard during the 6 January 2021 riots.
"The chant was: ‘Where’s Nancy?’" Mr Biden said, calling it "despicable."
"There’s too much violence, political violence," the President added, suggesting that election denialism and claims that COVID-19 was a "hoax" had eroded the political climate.
"Every person of good conscience needs to clearly and unambiguously stand up against the violence in our politics, regardless of what your politics are," he said.
Meanwhile, San Francisco Police Chief William Scott told a news conference that the attack on Mr Pelosi at their San Francisco home was "intentional".
He said: "This was not a random act. This was intentional. And it’s wrong."
Mr Scott declined to comment further on a possible motive for the assault and said the investigation was ongoing.
Mr Pelosi was being treated by doctors for bruising, severe swelling and other injuries.
Ms Pelosi’s spokesman, Drew Hammill, said he was expected to make a full recovery.
"The Speaker and her family are grateful to the first responders and medical professionals involved, and request privacy at this time," he said.
The attack raises questions about the safety of members of Congress and their families as threats to lawmakers are at an all-time high following the deadly Capitol riot.
It also comes just 11 days ahead of midterm elections in which crime and public safety are key issues.
In 2021, Capitol Police investigated around 9,600 threats made against members of Congress.
Other members have been violently attacked in recent years - former Democratic Representative Gabrielle Giffords of Arizona was shot in the head at an event outside a Tucson grocery store in 2011, and Representative Steve Scalise was severely injured when a gunman opened fire on a Republican congressional baseball team practice in 2017.
Members of Congress have received additional funds for security at their homes, but some have called for more protection.