The company's annual report shows his salary and performance-related bonus went from £450,000 to £600,000 to reflect his promotion from finance director.
But the value of long-term shares awarded to Mr Griffiths halved compared with the previous year, from £1.19 million to £597,311.
That dragged down his overall remuneration by 5.2 per cent, to £2.27 million in the 12 months to April 30.
This contrasts with the £3.44 million earned by Sir Brian Souter in his final year as chief executive.
The report shows Mr Griffiths earned 100 per cent of his available bonus, compared to a range of between 35 per cent and 64 per cent paid out to Sir Brian over the previous four years.
The new chief executive received his bonus in full after Stagecoach matched a group profit target of £214m and debt of £457m came in well below the £510m target.
The Perth company's annual report also shows that Sir Brian took home £201,000 in fees for his first year as chairman.
Finance director Ross Paterson was paid salary of £400,000, contributing to total earnings of £1.35m.
Mr Griffiths was last year awarded options on two tranches of shares with a maximum total value of £900,000 while Mr Paterson's award was a maximum £600,000, all vesting in 2016.
Mr Griffiths was promoted to the top job in May 2013 following Sir Brian's decision to step back from day-to-day management of the company he founded and grew to FTSE 100 proportions.