In 2007, he was awarded the Outstanding Young Scientists Award of the European Geosciences Union (EGU). He was the youngest scientist ever to receive this prestigious award. in 2010, he also received the prestigious Vening Meinesz Prize for young geoscientists and the Royal Netherlands Academy of Arts and Sciences Heineken Young Scientists Award for Environmental Sciences. In 2016, he received the James B. Macelwane Medal of the American Geophysical Union and in 2017 the Royal Netherlands Academy of Arts and Sciences Ammodo Award.

Sluijs was a (board) member of The Young Academy of the Royal Netherlands Academy of Arts and Sciences (2009 - 2014). He is an editor of the open access journal Climate of the Past, published by the European Geosciences Union.