Daijoji was built in 1261 by a warrior family to house an image of Dainichi (Vairocana). Since Dainichi is the main Buddha of esoteric practice, the patron asked a Shingon cleric to become the first abbot. In 1292 he invited Dogen's dharma heir Tettsu Gikai to come from Eiheiji as the new abbot and convert Daijoji to Zen. Gikai's student Keizan Jokin was one of the first to come and join him there, followed by Meiho Sotetsu and Gasan Joseki. Keizan succeeded as the abbot of Daijoji in 1298 but Gikai remained at the temple, providing instruction and guidance, until the end of his life.
While still practicing with his own teacher, Koun Ejo, the second abbot of Eiheiji, Gikai came to an understanding which helped to form his teaching style. Ejo (and Dogen before him) had criticized monks from the Darumashu sect who said that any and all actions embody Buddhism and that therefore no rules of conduct or behavior were necessary. He pointed out that this view left no room for the ethical basis of Buddhism. Gikai realized that there was an important distinction to be made between the belief that Buddhism encompasses all actions -- even evil ones -- and the understanding that all actions must be carried out as Buddhism. Dogen's position had been that it was Zen monastic routines that expressed inherent awakening, and Gikai now realized that there was no Buddhism separate from the wholehearted participation in monastic life; that one needed not only devotion to the care of other beings but a single-minded devotion to practice. His emphasis on the actualization of Buddhism within daily activities was passed on to his successors and may help to explain why he and his immediate followers did not emphasize the study of Dogen's texts. While Gikai did occasionally refer to the Shobogenzo when teaching his students, it was actions rather than words which he felt best expressed Buddha's teachings.
Gikai increased the frequency of rituals and chanting services as part of his leadership; because each ended with an eko, or dedication of merit, the purpose of these activities was clear and well-defined in the direction of merit toward some spiritual goal. We can see the reflection of this attitude in the Sanshin style: we keep forms simple in order to understand what we're doing and why, and to maintain their connection with zazen. Rather than being merely performances, our forms come from the mind of shikantaza as an expression of respect and gratitude.
Gikai's successor as Daijoji's abbot, Keizan, did not have the same close relationship with the temple's patron family as he had, and although two years after Gikai's death Keizan handed leadership of Daijoji over to Meiho, the patron replaced Meiho with a Rinzai abbot. Eventually he regained the post, but not during Keizan's lifetime.
By the time the last of Dogen's direct disciples died, about 60 years after he did, the Eiheiji community had several fairly independent branch groups centered around temples, including Jakuen and Giun at Hokyoji, Senne and Kyogo at Yokoan, Giin at Daijiji and Gikai and Keizan at Daijoji. Eventually Gasan consolidated his power at Sojiji while Meiho retained power at Daijoji, and a struggle ensued between these two Gikai disciples to determine which would be the head temple of his lineage; Sojiji emerged as the more powerful and would go on to become one of the two head temples of the Soto sect along with Eiheiji.
During the Edo period, our ancestor Gesshu Soku and his student Manzan Dohaku became the leaders of Daijoji and were heavily involved in the movement to reform rules and procedures of the Soto sect, including the method for dharma transmission. The temple became known as a center for strict training and was also the site of Manzan's work to compile the Shobogenzo. Over the centuries Daijoji was destroyed by war and rebuilt, then moved to its current location in 1697. About two dozen monks of all ages live and train there today.