More than 35,000 pottery fragments and other pieces were flown from Yale University to the Andean city of Cusco.
They had been taken to the US by archaeologist Hiram Bingham, who brought the site to international attention in 1911.
The move completes a deal signed in 2010, following legal action by Peru.
It argued that Bingham had only been loaned the artefacts.
The American archaeologist and historian took to Yale some 46,000 ceramics, bone fragments and metal pieces.
The first and second lots of artefacts arrived back in Peru last year.
The best pieces will now be on display in a newly built museum in nearby Cusco.
The citadel of Machu Picchu, located 2,500m (8,200ft) above sea level, was built in the 15th Century by the Incas.
It is Peru's main tourist attraction, attracting more than 1 million visitors a year.
By BBC News