Around 1777, Gilly married Friederike, a daughter of the regimental stable-master Friedrich Ziegenspeck. With her he had two children, Friedrich and Minna (who later married the politician Friedrich Gentz).

In Stargard, Gilly was in 1779 promoted to building director of Pomerania, before being transferred in 1782 to Stettin. As a building director, he designed (among other things) responsibly for the harbour company of Swinemünde