Marshall left "by mutual consent" this week with new chairman Stephen Murphy taking over until new owner Terra Firma finds a successor.
Marshall took over in 2008 after Bank of Scotland took over the company from Sir Tom Hunter and led GCG to a £276m takeover this year. Murphy praised Marshall for making GCG "market leader with a high-quality horticultural offering".
Garden Centre Association interim chief executive Iain Wylie said: "I'm as surprised as anyone. Things are changing at GCG. They are serious about the business and I hope they choose a course that will bring stability and they stay part of the wider industry."
HTA marketing director Andrew Maxted said: "All in the trade would recognise the turnaround that Nicholas led, in particular his putting plants back at the heart of the business, recognising the value of local brands and his success in creating the largest gardening club in the UK."
Terra Firma chairman Guy Hands said Marshall had stabilised the business and left a "strong platform for growth".
A company representative said Hands and Murphy evaluated the business and decided by mutual consent it was time for new leadership.
Marshall thanked staff for their loyalty. He ran Country Gardens before GCG (then Wyevale) bought it out in 2000, retaking control and renaming Wyevale in 2008.
See Garden Retail interview with former GCG chief executive Nicholas Marshall - linked below.