In 1780 Stibolt assumed the role of General Adjutant to the King, and he compiled several reports regarding the defensive structures on Christiansø. He also played a role in ship construction endeavors, notably contributing to the creation of the "unsinkable" defense frigate known as Hjælperen. This frigate was intended to participate in the Battle of Copenhagen in 1801.

However, Stibolt's professional journey was marred by conflicts with Henrik Gerner, a renowned master shipbuilder who was regarded as a superior designer. Subsequently, disagreements emerged with Hohlenberg, a student of Gerner who later became a master shipbuilder. These conflicts took a toll on Stibolt's well-being. Following Henrik Gerner's passing in 1787, Stibolt was appointed as the interim master shipbuilder for the Danish navy in 1788. This temporary position was later confirmed as a permanent role in 1790. Stibolt's impressive portfolio encompassed the design and construction of approximately 39 vessels of diverse types, in addition to 37 smaller boats. This collection included four ships-of-the-line, five frigates, and numerous smaller ships. Notably, Stibolt's ship designs continued to be utilized, even beyond his lifetime, with additional ships, particularly brigs, being built based on his designs.