The areas around Żebbuġ has been inhabited for millennia. There are Bronze Age remains on Ta' Kuljat hill, and even older remains can be found to the north, close to Qbajjar Bay. Punic tombs were also found at Qbajjar. Over the following centuries, the area was then inhabited only by a few farmers. A community began to take shape in the 13th century, and eventually, a small chapel was built. In 1643, plans were made to build a fortified city in Marsalforn, to serve as Gozo's capital instead of the ancient Cittadella, but the project was eventually abandoned due to a lack of funds.
The parish of Żebbuġ, which is dedicated to the Assumption of Mary, was established on 28 April 1688 by bishop Davide Cocco Palmieri. The village's parish church is one of the oldest churches in Gozo, after St George's basilica (1678) and the cathedral (1714) in Victoria.
From 1715 onwards, a chain of fortifications was built along the Żebbuġ coastline, especially at Marsalforn. Most of these have been destroyed over the years, with the only surviving vestige being Qolla l-Bajda Battery between Qbajjar and Xwejni Bays.
In 1738, deposits of calcite travertine or, though it is related to neither, were discovered in a field known as Taċ-Ċaqra or Is-Sagħtrija. The travertine was used to decorate the interior of the parish church of Żebbuġ, as well as in some other churches in Gozo and Malta.