The temporary increase in the threshold has meant that 95% of first-time buyers over the period have not had to pay stamp duty.
The Council of Mortgage Lenders estimated that 150,000 first-time buyers have benefited from the increase in the threshold over the past two years.
Halifax said that returning the starting threshold to £125,000 would result in nearly 45% of first-time buyers paying stamp duty.
The South East and Greater London benefited most from the change with around seven in 10 first-time buyers having to pay no stamp duty directly due to the raising of the threshold from £125,000 to £250,000.
The North an Northern Ireland saw one in six first-time buyers exempt from the tax as a result of the increase.
Only 4% of first-time buyers in Greater London will be exempt from stamp duty when the starting threshold returns to £125,000. Four in five first-time buyers in the South East will pay the tax.
Martin Ellis, Halifax housing economist, said: “The stamp duty holiday has directly helped four in 10 first-time buyers over the past two years.
“The doubling in the starting threshold has been a significant benefit to those who have benefited during a time of economic and financial difficulty for many.
“A first-time buyer making a purchase of £200,000 will see their buying cost increase by £2,000.”
