Resistance to Byzantine influences in the 11th c. weakened Armenia's independence while the Seljuk invasion in the 1060s and 1070s virtually wiped out the artistic achievements made under the Bagratids. The Seljuk invasion was particularly brutal, forcing monasteries and churches to be constructed in the most remote and inaccessible areas of the country, surrounded by large ramparts of stone. Khachkars continued to develop as the focus of religious and artistic energy was placed on small monuments it is no coincidence that this is a period of great development for the miniature and manuscript art as well. The stones were much easier to construct over churches, and manuscripts are the most portable art forms in Armenia's tradition.

In the 11th century complex geometric and flora decorations predominate to the point where they form a never ending line as they intersect with other patterns. Resembling the Celtic knot, which has no beginning or end, this symbol must have been a crucial expression of eternity for Armenians faced with brutal and humiliating defeats by Seljuk Moslems determined to wipe out their culture. This never ending line, in the course of its movement, transmutes from one form to another without defining the start or the end, and is both mind-boggling and dazzling to see.

Armenians began to break free from Seljuk domination in the 12th century, and a new renaissance began; churches, monasteries and Khachkars became more elaborate in design and details, while Khachkars began to be used for corporal as well as spiritual purposes, erected to mark military victories, to commemorate an event of historical significance, to dedicate the construction or renovation of churches, bridges, and other buildings, as well as the time-honored tradition of commemorating a major donation. For example, The Zakarian brothers, in the inscriptions on a Khachkar erected at Amberd in 1202 AD mention their victories against Seljuks. Another is Queen Vaneni, who commissioned the construction of a bridge at Sanahin and erected a Khachkar (ca. 1192 AD) to commemorate the memory of her dead husband, King Abas. Those set into the walls of a church tend to commemorate a donation or gift.

But of all reasons for carving a Khachkar, the most significant was as gravestone. As a part of the tomb, they complete the architectural form, especially mausoleum churches noted by their use of khachkars. Examples are a pair of khachkars standing on the western facade of the church mausoleum at Tzaghkatskar monastery (1041 AD, Vayots Dzor) and those at a three-altar tomb for the Ukani princely family in Haghbat monastery (1211-1220 AD, Lori).