The Scottish Government spent £56,378 on plants in 2012/13, up from £39,134 the previous year and £34,769 in 2010/11, figures obtained by the Liberal Democrats reveal.
The largest spend was at the directorate general for governance and communities, which is linked to Deputy First Minister Nicola Sturgeon's office, where spending rose from £18,600 to £33,816 in three years.
This rise was due to a new facilities management contract which renegotiated the price of office plants within the total price of the contract, according to the Scottish Government.
Ministerial private offices spent £26,000 on flowers in three years, leading to calls for ministers to "prune this growing spend" on plants.
Liberal Democrat business manager Alison McInnes said: "Scottish Ministers don't come up smelling of roses after spending more than £130,000 on pot plants and flowers in the past three years.
"At a time when people still have to tighten their purse strings, many will be surprised that the Scottish Government is spending this money cultivating plants when it would be better spent cultivating jobs."
A spokesman for Alex Salmond said: "Perhaps the Liberal Democrats should be more concerned with the fact they support an unelected House of Lords mired in an expenses scandal."