Debatable, though, is whether Elbasan was a town founded by the conquerors. As its Slavonic name of Koniuh suggests, this must have been an older settlement turned by the Ottomans into a fortification and a garrison town. In any case, there is evidence showing that, in order to support the rear of his army, Mehmed II built up in the valley of the Shkumbin River a huge fortress calling it Elbasan, that is to say stamping, trampling on the country. According to I. Duichev, there exist some marginal notes describing the foundation of the town of Elbasan. Thus, a  marginal note of 1466 tells about the deportation of citizens of Ohrid to the newly founded Ottoman town, and there is a record from the same year noting down the deportation of denizens of Skopje in order to settle in the new town. In reference to these events of founding and populating the town of Elbasan (Koniuh), there is also an extensive and valuably informative marginal note written by diak Dimiter of Kratovo, who copied a code at the demand of archbishop Dorotheos of Ohrid.³⁸   It is an undeniable fact that in the time of Sultan Mehmed II, when the town of Skopje was already losing its importance as a major strategic site in the Balkans, Elbasan, in the surroundings of which battles were still being fought, acquired a leading part in the imperial military plans and became a key site of Mohammedanism. Military garrisons and route detachments were stationed there, certain distinguished members of the local administration were established with their families as well. In fact, this was the Ottoman colonisation of Elbasan, because data about migration of ordinary households from Anatolia are lacking. 

There is some evidence that in 1467 Sultan Mehmed II deported from Skopje to Elbasan over fifteen Bulgarian households, probably for doubts as to their trustworthiness, or aspiring to intimidate the unruly Bulgarians in town. These must have been Christian müsellems, who had been brought to take part in the construction of Elbasan as masons, stoneworkers, or any other building workers.³⁹  In a similar way, the previous year the sultan also exiled some eminent Ohrid families. This was a result of the deterioration of the relations between the Ottoman administration and the Archbishopric of Ohrid. The Ohrid clergy and the city notables were keenly concerned with the struggle of the Albanians against the Ottoman occupation and were trying to find ways to support it. The archbishops Nicholas and Zachary took advantage of the opportunity of having to go to preach against the Florentine Union and departed for the Albanian lands, where they stayed for a long time with Skanderbeg in the fortress of Kruja. The persecution of the citizens of Ohrid and the expulsion of the ecclesiastics, with the archbishop in the lead, evidenced that the sultan suspected both of some kind of anti-state activity.⁴⁰  Undoubtedly, the policy of interning, banishment, and resettlement was a common practice for the Sublime Porte and traditionally a well-known procedure in the Balkans. 
Regardless of the Muslim character of the new town of Elbasan, it is unlikely for its population to have been homogenous in composition. In the 17th century the population of the city increased to the size of 2,000 households. This large number was due above all to native Albanians who had adopted Islam. One should not ignore evidence that it was precisely in Elbasan and its neighbourhood where the Crypto-Christians, Islamised Albanians professing in secret their old religion, were concentrated.