He returned to Denmark in 1764, and was named Building Inspector. That same year he was invited to join the academy, and received the assignment to design "
Et kongeligt Palais, liggende paa en smuk Plads" ("A royal palace located on a beautiful plaza"). His design was judged successful, and he was accepted as member of the academy in 1765, where he was given a job as Professor in Perspective in 1766. Between 1766 and 1769 he built the memorial chapel for former
Lord High Steward Count Adam Gottlob Moltke at
Karise Church in
Faxe, which had been begun by his former teacher and now fellow Professor at the academy architect
Nicolas-Henri Jardin. In 1770 he was named Royal Building Master to the court of King
Christian VII. In 1771 Professor Jardin requested that Harsdorff be named his successor as Professor of Architecture at the academy, which position he filled that year after Jardin vacated the position on 26 March in conjunction with his leaving Denmark to return to France. As professor he played an important role in the classical education of the next generation of architects. His students included
Peter Meyn,
Joseph Christian Lillie and
Christian Frederik Hansen. Harsdorff also became a member of the Main Building Directorate (
Overbygnings direktionen) in 1771. In 1773 he designed the pulpit at Our Saviour's Church (
Vor Frelsers Kirke) in the
Christianshavn district of Copenhagen. The neoclassical wood pulpit is painted to look like golden marble, and features a
frieze attributed to
Johannes Wiedewelt and
Peder Als. That same year he rebuilt in the King's Garden (
Kongens Have), the gardens at
Rosenborg Castle in Copenhagen, the temple-like Hercules Pavilion for which Johannes Wiedewelt's studio produced the reliefs of
Hercules and
Omphale. The pavilion now houses a café. He also was commissioned to enlarge the
Nicolai Eigtved-designed
The Royal Theatre (1748) on
Kongens Nytorv that year. In the course of his work on this project he received permission to develop the site between the theatre and Charlottenborg Palace, home of the Art Academy, which he then developed 1779–1780 as a home for his family. Rebuilding of the theatre was carried on 1773–1774. In 1774-1779 he designed and started building the austere memorial chapels for
Christian VI and
Frederik V at
Roskilde Cathedral. Work on this project, however, was stopped in 1779 because of lack of money. The work began again many years after his death, and was completed by his student
Christian Frederik Hansen (1820–1825). Harsdorff acted as the academy's Director 1777–1779, and was named to the title of
Justitsraad in 1778. In 1779-1780 he designed and built
Harsdorff House at
Kongens Nytorv 3–5, which became the new model for Copenhagen townhouses of the time. The building is shown on a Danish postage stamp, part of series entitled Danish Houses which features significant Danish buildings. The building is now owned by real estate company
Karberghus. The tenants include the Harsdorffs Hus Office Club. Between 1781 and 1785 he designed the interior design in two large rooms at The Royal Library. In 1781 he was named Head Royal Building Master. Between 1794 and 1795 he designed and built the colonnade at
Amalienborg Palace to connect the recently occupied King's palace, Moltke Palace, with the Crown Prince's residence, Schack's Palace. In 1795 he was asked to create plans for
Frederik's Church (
Frederikskirke), now known as The Marble Church (
Marmorkirken), work on which had been halted 1770 after French neoclassical architect Nicolas-Henri Jardin had led the effort. Harsdorff created two plans, and made a model of one of them. The project was approved, but Harsdorff health was now weak. The work eventually was developed according to plans by
Ferdinand Meldahl (1827–1908). {{cite web|url= https://biografiskleksikon.lex.dk/F._Meldahl ==Personal life==