In the summer 2019, Bøndergaard joined Silkeborg IF from Ringkøbing IF.[2] However, Bøndergaard played, already a year before the switch, on a so-called 'double license', where he trained 1-2 times a week in Silkeborg while still playing for Ringkøbing.[3]
After joining the first team squad for a training camp in Spain in February 2023,[4] Bøndergaard made his official debut for Silkeborg on 6 April 2023, when he came on for the last few minutes in a cup match against SønderjyskE.[5] On 29 May 2023, he made his Danish Superliga debut in a match against FC Midtjylland.[6] On 10 August 2023, Bøndergaard extended his deal with Silkeborg until June 2027.[7]
In June 2024, Bøndergaard, along with teammate Oscar Fuglsang, was loaned out to Danish 1st Division club Fredericia for the upcoming season.[8] In his first six games for Fredericia, Bøndergaard scored nine goals in all tournaments.
