In 1972 a small group of graduate students at Syracuse University began meditating together once a week. Interest in zazen increased when the Venerable Eido Tai Shimano Roshi, then abbot of the Zen Studies Society's International Dai Bosatsu Zendo in the Catskill Mountains and New York Zendo Shobo-ji in New York City, was invited to lecture at the university by religion department professor Richard Pilgrim.

Eido Roshi returned to give a public talk the following year, and dedicated the small room the students were using in Community House, an annex of the university's Hendricks Chapel. He named it "Hoen Zendo," Dharma Salt Zendo, in recognition of the area's nineteenth-century salt industry that gave Syracuse the nickname "Salt City." Two of the students, Robert Strickland and Howard Blair, began attending retreats at New York Zendo Shobo-ji and the mountain monastery, International Dai Bosatsu Zendo. On staff at the monastery were Shinge Roshi and her first husband, Louis Nordstrom.

They moved to Syracuse in 1976, and under their leadership, the practice grew steadily. Two years later, when the university ended its sponsorship of the building, Hoen Zendo entered its gypsy phase, moving to various members' homes and a church basement. In 1984, Shinge Roshi transformed the attic of her university area house into a zendo, and Hoen Zendo was newly established there. During the years that followed, many guest teachers visited, including John Blofeld, Paul Reps, Masao Abe, Huston Smith, DaiEn Bennage, and Maurine Stuart, who traveled from the Cambridge Buddhist Association in Massachusetts to lead sesshin twice a year until her death in 1990. The Syracuse Sangha grew slowly but steadily, and the practice and appreciation of Zen Buddhism deepened.

In 1989, Hoen Zendo was incorporated as the Zen Center of Syracuse, with Shinge Roshi as its spiritual director. At Shinge Roshi's ordination in 1991, Eido Roshi changed the character En in Hoen from salt to connection, symbolizing the unbreakable in nen — affinity link — existing between him and Shinge Roshi, between his lineage and the Syracuse sangha. He also added ji to the name, in recognition of a temple in the authentic tradition of Zen Buddhism.

During the next few years, three of Shinge Roshi's students were ordained: Saigyo Terrence Keenan, a poet and rare books librarian at Syracuse University; and Doshin David Schubert and Entsu Scott Rosecrans, who went on to train as monks under Eido Roshi at Dai BosatsuZendo and at Shogen-Ji in Japan.

In 1993 the Zen Center of Syracuse Hoen-ji organized a national conference celebrating the centennial of Zen in America. Eido Roshi gave the keynote address, and teachers, practitioners, and visitors from all over the country congregated for the four-day historic event, in which significant issues in the transition and transmission of Buddhism to the west were discussed. Art work by Mayumi Oda and Kazuaki Tanahashi and calligraphic scrolls by Hakuun Yasutani Roshi, Soen Nakagawa Roshi, and Eido Shimano Roshi were exhibited at the Everson Museum of Art as part of the conference.

Hoen-ji continued to expand and develop its programming, and by the early nineties, it was clear that a larger facility was necessary. After a long search, the group found the perfect site, in an historic section of the city. Members of the Zen Center of Syracuse enthusiastically took on the challenge of acquiring the beautiful property at 266 West Seneca Turnpike. With a flurry of renovation work, including the restoration of the carriage house as the new zendo, practice began there in July of 1996. Three years later, with its membership and programming growing steadily, the center was able to purchase the neighboring property as a Buddhist student residence. Two more students were ordained: Jikyo Bonnie Shoultz, Buddhist chaplain at Syracuse University; and Gyoshin Virginia Lawson, a chaplain at SUNY Upstate Medical University.