Downey, who is the current publishing director for Viz, Poker Player and Inside Poker, took over from Mallinson a fortnight ago when Monkey was moved from Dennis Publishing's new product division into consumer magazines.
The restructure has left Mallinson without a job.
Downey said: "It is an incredibly exciting time for Monkey at the moment, and no one can deny James the work he has done in making the format really take off - 2008 is already shaping up as a huge year. It is my job to make Monkey even bigger and better."
Downey added that Dennis was now looking at expanding the Monkey brand into other media platforms, including mobile.
Speaking from America, Mallinson said he had no regrets, despite moving to Monkey from Emap only about six months ago.
He said: "I'm really proud of the work I have done and what I have achieved at Monkey. I leave with my head held high and no bitterness.
"Six months ago, the brand was not something everyone was confident in, but I have left the firm on a very sound financial footing."
According to ABCe figures, monkeymag.co.uk had 268,000 unique users in January.