Morgan Ellis started his career in 2008, when he was drafted in the third round of the QMJHL draft by the Cape Breton Screaming Eagles, and stayed a permanent part of the Eagles for five seasons.
In 2010, the Montreal Canadiens drafted him 117th overall, in the fourth round of the NHL Entry Draft. That same year, he became the team captain and top defenceman for the 2010-11 season with the Eagles. In 65 games, he tallied 34 points (eight goals, 28 assists) — both tops among Cape Breton defencemen.