The UK Civil Aviation Authority (CAA) put on 567 flights which brought back 83,875 passengers to the UK after the travel company went into administration.
The last of the flights – a service from Tel Aviv in Israel with 122 passengers – landed at Luton Airport at just after 3.30am on Monday.
The CAA said it is contacting all 1,000 Atol protected passengers still abroad “in order to arrange alternative flights to get them home when their trip has ended”.
A spokesman for the regulator told the Press Association the operation is expected to cost “in the region of £60m”.
Andrew Haines, CAA chief executive, said: “This has been a phenomenal challenge and one that has required the cooperation and support of many businesses, government departments and individuals.
“It was a very sad day when Monarch went into administration and our thoughts remain with all the Monarch employees who have lost their jobs.”
He added 98pc of passengers arrived home on the day they were scheduled to return.
Administrators KPMG said 1,858 of around 2,100 people employed across Monarch’s airline and tour group had been made redundant after the firm went bust.
Nearly 100 of those made redundant were employed by Monarch Travel Group, while 1,760 were employees of Monarch Airlines.
The remaining employees will help with the administration process, and assist the CAA in bringing holidaymakers abroad back to the UK, KPMG said.
Atol was the UK’s holiday financial protection scheme and costs £2.50 per customer. By law every UK-based travel company that sells air holidays has to have a licence.
The largest Atol company to stop trading before Monarch was XL Leisure Group in 2008, which had 43,000 people abroad at the time.