Malcolm Wilson arrived at Georgetown as a project player, having averaged 6.3 points per game at Ridge View HS in Columbia, SC. A player seen with potential to mature in the pivot, Wilson chose Georgetown over offers at South Carolina and Clemson.

The jump to the college level was a significant one: Wilson did not see any game action his freshman season, and broke his leg in practice entering the final week of the 2019-20 season. As a sophomore, he saw glimpses of improvement, including three rebounds and a blocked shot versus Syracuse.

Following the transfer of Qudus Wahab in 2021-22, Wilson platooned with Timothy Ighoefe with 10 starts at center, but his slender build made it difficult for him to compete against stronger opponents. A career high of 13 points and eight rebounds against Howard was a season high, but his time was severely limited during Big East play. Wilson played in just 93 minutes in conference play and averaged 1.3 points and 2.3 rebounds a game.

Malcolm Wilson's status for his senior season was the subject of speculation following a total of nine players signed by head coach Patrick Ewing in the off-season, putting Georgetown over its 13 available scholarships. In September 2022 Wilson was reassigned as a team manager and was later returned to the roster following the mid-season transfer of Dante Harris.

A 2023 graduate, Wilson exercised a grad transfer option at Queens University (NC) for the 2023-24 season.