His working dinner with President Emmanuel Macron on Thursday came amid spiralling energy prices and fears over Iran’s nuclear programme.
The prince denies approving the killing at the Saudi consulate in Turkey.
Khashoggi’s fiancée said she was outraged by his visit.
Hatice Cengiz accused President Macron of receiving her late partner’s “executioner with all the honours”.
Mohammed bin Salman flew into Orly airport, south of Paris, the night before the talks and stayed at a luxurious château at Louveciennes, west of Paris.
A cousin of the murdered journalist, Emad Khashoggi, designed the Château Louis XIV as a tribute to the so-called Sun King who ruled France in the 17th Century.
Hours before the two men were due to meet at the Elysée Palace, three campaign groups filed a criminal complaint accusing the prince of complicity in Khashoggi’s torture and murder.
Among the plaintiffs was Democracy for the Arab World Now (Dawn), which argued that Mohammed Bin Salman (MBS) did not have immunity from prosecution, as he was not a head of state, and France was one of the only possible venues for justice.
Bénédicte Jeannerod of Human Rights Watch said that without securing “strong and concrete commitments” on rights, Mr Macron risked rehabilitating MBS and “whitewashing” his image.
Ahead of the meeting, an aide to the French president promised that human rights would be raised “in a general way”, but said it was important to talk to all of France’s partners to solve the problems that all of Europe faced.
The two men have met since the Khashoggi murder, including in the Saudi city of Jeddah last December.
Prime Minister Elisabeth Borne said she did not think the French people would understand it if their president did not talk to the world’s energy producers when tensions over prices were high and “Russia cuts gas supplies, threatens to cut them and then cuts them again”.
Russia’s invasion of Ukraine has sent energy prices soaring and President Macron has urged Saudi Arabia to boost oil production.
The oil producers’ group Opec+, which includes Russia, meets next week and its members have come under pressure to help ease the crisis.
US President Joe Biden was pictured giving the prince a fist-bump during a visit to Saudi Arabia earlier this month aimed at rebuilding relations.
The prince has always denied involvement in the journalist’s death and Saudi prosecutors have blamed “rogue” Saudi agents.
US intelligence agencies said he had approved the operation. A UN inquiry concluded that Riyadh was responsible for an extrajudicial killing.
