Despite being praised by many for his overall performances, Miller failed to score in his first nine games for Celtic. He finally scored his first goal, against Old Firm rivals and former employers Rangers at Celtic Park in September 2006. He then went on to score in Celtic's 1–0 Champions League win against Copenhagen from the penalty spot and scored two in the 3–0 win over Benfica. By scoring in the 2006/07 Champions League season, Miller became the first player to score goals in the Champions League for both Rangers and Celtic. However, he ended the season with only four league goals. He did play in the 2007 Scottish Cup final, before being substituted because of an injury. Despite hints from the player himself that he would leave to get more first-team opportunities, Miller vowed to stay at the club and fight for his place at the club. Miller scored his first goal in his first appearance of the 2007/08 season in a 4–1 victory over Falkirk and added to his collection the following week by scoring against Aberdeen. He scored 11 goals in total for the club in 46 appearances.