King Charles met Yousaf during an audience at the palace.
During his visit to London, Mr. Yousaf also met with the Spanish Ambassador and the Mayor of the City of London. On Tuesday he met with the Irish Consul General.
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Yousaf has previously said he is a Republican and attacked coronation-related costs earlier this month, saying he expected them to be limited as a result of the cost-of-living crisis.
He and his wife Nadia El-Nakla attended the coronation on May 8.
The meeting comes after the Stone of Fate was returned to Edinburgh Castle earlier this week.
Traditionally, the stone was used to crown monarchs of Scotland but now it is used to crown the monarchs of the United Kingdom as part of the coronation ceremony.
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Former Prime Minister Alex Salmond suggested that the police should have been used to prevent the stone from being moved from the castle, which Yousaf dismissed.
The FM said: “Alex Salmond must remember, of course, that operational matters are for Police Scotland.
“It is not for the Prime Minister to tell the police what to do, but of course it would not have been the right thing to do even if those powers existed.
“Alex Salmond can sit there and talk about the Stone of Fate all day. It seems that’s all he’s been talking about for the past few weeks.
“I pledge to talk about reducing poverty, the cost of living crisis, investing in our public services.”