[1] After his return to Denmark in 1865, Bønecke settled as a master mason in Copenhagen but soon received a considerable amount of architectural assignments.

In 1871, in collaboration with V. Friederichsen, he won third prize in the competition for the new Royal Danish Theatre at Kongens Nytorv.

Their first collaboration was on an orangery (known as Pompeii) completed in 1876 for Jacobsen's home, now known as Carlsberg Academy.

In 1885, he designed the small Well House in the Royal Danish Horticultural Society's Garden.

Bønecke married Augusta Vilhelmine Lorentze née Biørn on 3 June 1866.