Beginning in the second half of the 9th century, as the Arab caliphate weakened, political power was restored to Armenia with the founding of new kingdoms: The Bagratuni in Ani (North and central Armenia), the Ardzruni in Vaspurikan (Western Armenia), and the kingdom of Kars and the Dzagikian Dynasty in Siunik. From the 9th century, the cities of Armenia (Ani, Lori, Kars, Kapan and Van) began to flourish. Monasteries and cloisters were founded throughout the country (Tatev, Sevan, Geghard, Gndevank, Sanahin, Haghbat). The struggle for liberation from Arab domination in the 8th-9th centuries and part of the 10th century, was closely linked with the idea of the crucifixion and resurrection of the son of God, who was martyred for the salvation of mankind. It was during this period that Khachkars appeared in their current form.

While the name "Khachkar" translates into "Stone Cross" and that would seem enough to qualify any stone carving of a cross as a Khachkar, experts consider the real beginning of the Khachkar in 879 AD, when the wife of Ashot Bagratuni, Queen Katranide, commissioned a Khachkar at Garni "in mediation" for her soul. It is in this period that the design of the Khachkar achieved its first golden era. If the purpose of the Khachkar in earlier centuries were to represent the triumph of the church over paganism (and politically to assert Armenia's nationality in the face of hostile neighbors), then the 9th-11th centuries were a period of relative peace and prosperity, and the focus changed to secure the salvation of the individual soul. Khachkars from this period became not only Christian monuments, but individual memorial monuments.

One example is the 881 AD Khachkar erected at the Mets Mazra village in Vardenis region in memory of Grigor Amirnerseh, the prince of Siunik and Aghvan. Others were placed in Nerkin Talin, and inside the St. Hripsimeh and St. Guyaneh memorial churches near Martiros in Vayots Dzor. These monuments were basically "stone prayers," meant to send perpetual supplication on behalf of the donor. The stones are noted for their generalized forms, the linking of vignettes (grapes, palm leaves, the tree of life), and a sensitivity for harmonic symmetry which gives a lightness to the immense monuments. Other experiments in design are continued rounded flagstones on which the cross is engraved with equal arms.

Another influence in the 9th century were pictures of church benefactors on their facades, holding a model of the church. Examples include Giurgeh and Smbat on Sanahin's Amenaprekich and Haghbat's St. N'shen Church, and Gagik Bagratuni at St. Grigor church in Ani. As donations were given to monasteries, shrines and khachkars were erected in memory of the donor.

The overall design of the Khachkar can be traced to the 9th century, with a cross (resting on a rosette or sun disk design) carved in the center of the image. The remaining surface is covered with complex patterns of flora or geometric engravings. The facade is bound with a border formed from non-repeating geometric rosettes, and the entire design was sometimes crowned with an original cornice under which thematic portraits were carved showing the Annunciation, John the Baptist, the Madonna, angles, apostles and saints, even the picture of the Khachkar donor.