A national minute of silence started and ended with a cannon firing from Edinburgh Castle.
First Minister Nicola Sturgeon led those paying their respects, hailing Prince Philip’s “longstanding ties to Scotland”.
She was among the many across the country to mark a silence at 3pm and Ms Sturgeon said: “On behalf of the people of Scotland, I once again express my deepest condolences to Her Majesty the Queen and members of the royal family.
“The many tributes paid to the Duke of Edinburgh in recent days have shown the depth of his contribution to public life over more than 70 years as well as his longstanding ties to Scotland.
“Many have reflected on his distinguished wartime record, his commitment to countless charities and organisations, and his love and support for the Queen throughout their marriage.
“Today, as the Queen and the royal family mourn the death of a loved one, we take this opportunity to celebrate and honour an extraordinary life.”
Pupils at the duke’s former school paid tribute to him by laying a wreath at sea in his memory.
Gordonstoun school remembered the duke during an event at Hopeman Harbour in Morayshire.
Prince Philip’s personal standard was raised at the summit of Ben Nevis by members of the Outward Bound Trust while fire crews paraded in silence at stations across the country.
Edinburgh’s Lord Provost councillor Frank Ross stood in silence at the City Chambers , leading the capital’s mourning for its duke.