The 26-year-old joined Boro from the Italian side last summer in a £12m move, but could not prevent their relegation back to the Championship after one season in the Premier League.
In a statement on the official club website, the Teessiders wrote: "The move is a permanent one, with Atalanta re-signing the player they sold to us a year ago. Everyone at MFC wishes Marten all the best for the future."
Boro also confirmed that the fee paid by Atalanta is undisclosed due to a privacy clause in the contract, but Sky Sports News believes that it is in the region of £13m.
De Roon, who made his senior debut for the Netherlands last year, played 33 times last season for Boro in the top flight, scoring four goals.