From June 4, all hot drinks bought at the associated buildings' cafes will be served in reusable mugs.
Those consuming hot drinks inside will be provided with ceramic mugs. Staff are being urged to bring their own cups to take away.
Environment Secretary Roseanna Cunningham said: “The Scottish government is determined to lead by example when it comes to tackling the scourge of plastic littering our countryside and polluting our seas.
“We support the EU’s vision to reduce single-use plastics as far as possible and ensure any single-use plastics are easily recyclable by 2030. We are currently considering what other single-use items can be reduced and removed from Scottish government buildings later this year.
“Our newly appointed expert panel is considering what further action we can take to fight against our throwaway culture, and this will include looking at disposable cups and plastic straws as well as any potential implications for disabled people.”
Sodexo employees provide catering for Scottish government staff.
Those affected by the changes were notified at the beginning of May.