After the retirement of Erik Norman Svendsen as Bishop of Copenhagen in 2009, Skov-Jakobsen was chosen as one of the six candidates. He lost the first round to the Secretary General of Kirkefondet Kaj Bollmann who got 257 votes against Skov-Jakobsen's 214. In the second round of elections only Skov-Jakobsen and Bollmann remained. Skov-Jakobsen got 608 votes against Kaj Bollmanns 353 votes. He was installed as Bishop of Copenhagen on 31 August 2009 in the Cathedral of Our Lady in Copenhagen as the sixth bishop since the diocese was established in 1922. On 1 January 2010 he became a Knight of the Order of the Dannebrog.