Ishak Bey mosque was built by the famous ruler of Skopje - Ishak Bey, who in the first half of the fifteenth century, in 1438, in addition to the mosque as its memorial, erected another mausoleum, madrassa, mansions and buildings that belong to the profane architecture.
In 1519 the mosque was adjusted and then were added two lateral vessels, by the Mehmed son Haji Dzindzi (Хаџи Џинџи), grandson of Ishak-Bey. This is preserved on inscription of the north portal. This mosque known also as the "Great" Mosque, was completed by Mehmed, the son of Haji Dzindzi, at the end of the muslim month Hidzhar in 925 (1519).
The mosque suffered damage in fire in 1689.
Aladja, which means colorfull, the mosque was named by the inscripted colorful tiles, which were preserved until 1689, and today there are still on the turbe behind the mosque, with which were decorated the outer walls.
Of secular buildings, which were built simultaneously with the mosque, preserved is only six sided turbe, with nicely staged dome, covered with lead. According to one legend, in the turbe was was buried the treasurer of Ishak Bey. Interesting is the sarcophagus (tabut) with two marble tombstones mark the tomb underneath builded from baked bricks.