Returning to Scotland, Goodwillie briefly played for Caledonian Amateur League team Doune Castle. In March 2017, he joined Scottish League Two side Clyde on a short-term contract until the end of the 2016–17 season. Clyde's decision to sign Goodwillie attracted criticism, as politician John Mason said he would no longer attend their games for the rest of the season. Goodwillie made his debut for Clyde against Cowdenbeath on 1 April, coming on as a 66th-minute substitute for Peter MacDonald. On 15 April, Goodwillie scored a hat-trick for Clyde in a 3–2 win against Elgin City.