In 1391 Yigit-bey conquered Skopje. Since the people of Skopje fiercly resisted, the Ottomans ravaged the city and pars of the city walls. After these events, the Kale acquired a new character and was used as military barracks.
With the research along the southern wall a renewal of the crown of the medieval wall was discovered, as well as numerous foundations of stone buildings, warehouses, workshops and barracks, most probably for the needs of the Ottoman military squad.
After the demolition of the southern gate, the same was fully reconstructed for the new military needs. The two lateral towers were generally expanded and erected in the upper sections, and the space between them was closed with a new wall. A new passage was set, half-way narrowed with a threshold erected at about 2.50 m higher than the previous one. Because of the amassed debris layer and the embankment from within, the street along the wall (via sagularis) was enclosed by wall-railing and a new main entrance street which leads straight to the top, to the higher parts, in the yet unexplored area of the terrain.
The inventory in the discovered constructions from this time document activities common for a fortress of this character.  
The border of the Ottoman Empire was soon moved far to the north and the Skopje Fortress lost its military-strategic significance, except for being barracks area for a small military crew.
In the north-eastern part of the fortress numerous pits dating from this period were found which were used for extracting clay, and later as waste pits filled with the waste and refuse from the near craftworks workshops. The items found in these are small items for home use, animal bones, broken iron tools, slag from metal melting, candlesticks, and most of all pieces from broken, semi-fired or misshaped jugs, plates, vases, and other pots, as well as decorative glazed tiles used for building the fireplaces.
The sultan Bayezid I (1389-1402) and Mehmed II (1444-1481) are the first Ottoman rulers confirmed by numismatic evidence. However, through the following centuries of ottoman dominion there is a strongly expressed lack of coin circulation on the Skopje Fortress. Obviously these had no significant economic, trade or commercial value.  

In the autumn of 1689 the Austrian army led by Piccolomini took over Skopje. The military report sent to the emperor in Vienna says that the Skopje Fortress was semi-demolished, poorly defended with 12 neglected towers and weak defence trench (to the east). It took only 400 horsemen to conquer the fortress in one assault. This report is quite opposite of the poetic account left by Evlia Celebi from the same period.
The archaeological finds, discovered by means of our research confirm the Piccolomini report. 

An inscription built into the eastern wall, dating from 1700, speaks of a great renewal of the Kale. The research led us to the conclusion that this happened indeed. Among other things, the greatest undertaking was the building of the great external wall. In front of the front eastern and southern wall the new surrounding wall, or fore-wall was fully built, with new monumental towers and embrasures. On the western end of the surrounding wall a new entrance was made towards the river Vardar, as well as a new main access to the Fortress through a monumental ramp  and a gate which led from the sub-city area – the Bazaar though the old eastern wall. The old southern gate lost its previous significance.
The archaeological finds document continuation of the military character of the Fortress. Near the south-eastern tower remains of blacksmiths were found and by them pieces of old guns, prepared for melting and reforging. Many of the pieces were half melted. Frequent finds from this period are the numerous ceramic pipes.