Ayvalık in the northwestern coast of Turkey is renowned with its characteristic architecturalheritage from the 19th-20th centuries. While some of its landmarks were recently restored and received newfunctions, some were lost in time due to natural and man-made damages. Correspondingly, this articlefocuses on two Greek Orthodox churches on Cunda / Alibey Island in Ayvalık that were demolished in themid-20th century, namely Panagia and Agios Panteleimon. The literature that mostly relies on scantsecondary sources and old photographs has very limited information about their long durée from an urbanand architectural perspective. Meanwhile, the plots of both churches appear as abandoned ruin sites withinthe urban fabric of Cunda today. In this article, the architectural history of the aforementioned buildings weresubstantially elaborated through a group of late 19th century archival documents with plans and drawingsthat were studied for the first time. In addition, published primary sources were considered and discussed.Then, their current preservation status were demonstrated after the most recent Cunda conservation masterplan and listing registries. Major outcomes have displayed that the timeline as well as architecture of Panagiaand Agios Panteleimon significantly differ from what has been previously put forth by the literature. Therewere successive alterations with intriguing irregularities until their final appearances by the end of the 19thcentury. Furthermore, their plots were almost completely omitted from the conservation point of view and areunder risk, though a multilayered architectural heritage is evident beneath the high debris and vegetation.