At the start of the 2006–07 season, Emanuelson played the whole game, as Ajax beat PSV Eindhoven 3–1 to win the Johan Cruyff Shield. He quickly regained his first team place, rotating in the left–back position and midfield positions. However, Emanuelson played in both legs of the third round of the UEFA Champions League against Copenhagen, as the club were eliminated following a 4–1 defeat on aggregate. On 14 October 2006 he scored his first goal for Ajax, in a 3–2 win against FC Groningen. This was followed up by helping the club keeping three out of the four consecutive clean sheets, in which Emanuelson played in the left–back position. In a match against Sparta Prague, Emanuelson was sent–off for a second bookable offence, as they drew 0–0. Despite this, he then scored his second goal of the season, in a 6–0 win against Willem II on 3 December 2006. By the end of the year, Emanuelson was nominated for the Golden Boy, but won the 2006's Amsterdam Talent award. He continued to start in the first team until a knee injury sustained during a 4–1 win against Feyenoord on 4 February 2007 saw him sidelined for a month. On 4 March 2007 Emanuelson made a return to the starting line–up, in a 1–0 loss against SC Heerenveen. This was followed up by setting up two goals, in a 4–1 win against FC Twente. On the last game of the season against Willem II, Emanuelson scored his third goal of the season, in a 2–0 win. Once again, he played four times in the newly born Eredivisie play-offs after finishing in the second position in the regular competition. In the play-offs, they defeated Heerenveen and AZ Alkmaar to claim a spot in the Champions League preliminaries for the following season. Emanuelson was featured in the KNVB Cup Final against AZ, playing 120 minutes and finishing 1–1 as Ajax went on to lose 8–7 as a result and win the tournament for the second time in a row. At the end of the 2006–07 season, he went on to make forty–six appearances and scoring three times in all competitions.