The president's doctor, one of his nieces and an ex-minister of commerce have been charged with conspiracy and attempted murder, officials said.
Prosecutors said the president's niece and his doctor were offered 1bn CFA francs (Â£1.2m; $2m) to poison him.
The three have been remanded in custody, officials say.
Prosecutors yesterday named them as Dr Ibrahim Mama Cisse, the president's niece Zouberath Kora-Seke and former minister of commerce Moudjaidou Soumanou.
Authorities said they also intended to issue an arrest warrant for businessman Patrice Talon, a former ally of Mr Yayi who fell out with the leader.
Chief prosecutor Justin Gbenameto told reporters that the alleged plot started on 17 October while the head of state was on an official visit to Brussels.
He said the president's niece, who accompanied him on that trip, was approached by Mr Talon who offered her money to administer drugs to the president, provided by his personal doctor.
Two days later the poison arrived on a flight from Brussels, he said. The prosecutor said that medicine which the president usually took was then replaced with the poison.
It is alleged that Mr Soumanou acted as an intermediary in the affair.
But Mr Gbenameto said the plot failed because the president's niece informed her sister and others who then alerted the president.
The three defendants were arrested on Sunday.
Mr Gbenameto stated that the judiciary remained independent and he urged people to remain calm.
Mr Yayi, 60, was first elected president in 2006 and re-elected last year. He is currently chair of the African Union.
In 2007, he survived an ambush by gunmen who attacked his convoy during an election campaign tour.
Three people plotted to kill Benin's President Thomas Boni Yayi by substituting poison for his medicine, prosecutors say.