The move will see European services to Paris and Amsterdam cut with only London remaining. The two direct services will end in January.
Under the new agreement Malaysia Airlines will add its code on Emirates flights to Europe, Middle East, Africa and the Americas.
In return, Emirates will add its code on Malaysia Airlines flights to within Malaysia, south-east Asia and selective cities across the Asia-Pacific region.
Malaysia Airlines chief executive Christoph Mueller said: “This partnership gives our customers access to a dramatically expanded range of travel options.”
The new deal expands on the two carriers’ existing interline agreement and offers up around 90 destinations.
Speaking during last month’s WTM, Mueller said the carrier would be looking to grow closer to home.
The former Aer Lingus boss came in with the company still reeling from the loss of two aircraft in 2014.
He has cut both jobs and routes and is also planning a rebrand all in an attempt to return the carrier to profit.
