In 1953 Jones returned to Fayetteville to teach in the architecture program. Much of his energy in the following decades was devoted to teaching design and architectural history. In 1955, he designed his own house, and there soon followed several commissions by faculty at the university for homes. In the 1960s and 1970s Jones was building residences at the rate of one to four per year, most in Fayetteville or northwest Arkansas, but also some in surrounding states.

Although some of these houses received national awards from the American Institute of Architects (AIA), it was not until the Thorncrown Chapel was built that Jones was widely recognized as a significant 20th-century architect. The AIA considered that building one of the best of the 1980s, and its success led to commissions for additional small religious buildings and more residences in following years.

The Thorncrown Chapel was designed as a place of quiet retreat near Eureka Springs, a busy tourist mecca. Made of wood and glass, it harmonizes with its isolated environment. The surrounding forest and the sky overhead can be seen through its glass; it is a place where the outside is inside. The floor is stone, and metal is used for some details. A small building (24 by 60 by 48 feet), it is nevertheless a dramatic space. Jones' emphasis on natural materials, and his making the outdoor setting a part of the interior experience are characteristics found in Wright's work, in which organic forms tie together different spaces. It cost only $150,000 to build and seats 115.

Thorncrown Chapel proved to be such a popular site for weddings and worship services that its role as a place of contemplation was threatened. Jones was then commissioned to design the Thorncrown Worship Center (1989) nearby. It is a larger building designed for more formal functions but, like its sister building, uses natural materials, and its open ends allow the Ozark mountain scenery to become part of the interior experience.

In a radio interview in 1994, Jones said there is a religion to his architecture. "I like to think of myself as being concerned with a higher order of things and probably the clearest manifestation we have of some higher order in the universe is wheat we see in nature and what we feel in nature."

The success of the Thorncrown Chapel led to other commissions for similar small religious structures. They include the Mildred B. Cooper Memorial Chapel (1988) in Bella Vista, Arkansas, which features steel beams fashioned in gothic arches; and the brick and wood Marty Leonard Community Chapel (1990) at the Lena Pope Home, Fort Worth, Texas. Both the Pinecote Pavilion for the Crosby Arboretum near Picayune, Mississippi (1987), and the tiny Pine Eagle chapel at a Boy Scout camp near Wiggins, Mississippi, seem to float above the water and with their openness and airiness recall Japanese pavilions. This similarity is again reminiscent of Wright's interest in oriental architecture and its relationship to surrounding nature.

In 1997, it was announced that Chapman University in Orange County, California, would build a new chapel designed by Jones at the center of the campus and it would be called the Wallace All Faiths Chapel.

He has had residential commissions in more than a dozen states from Massachusetss to Michigan. Jones' houses emphasize natural materials, a close relationship to the landscape, and easy movement from one space into another. Normally light fixtures and cabinetry are especially designed for the interiors. Fountains, skylights, hearths and fireplaces, and large windows are found in Jones' interiors, and a concern for craftsmanship is evident in the details.

Jones once said, "I felt I was somewhat outside the pale" in terms of contemporary architecture. That he limited his practice to small-scale structures and spent much of his career in the classroom, kept him from full recognition of his talent until late in life. He might be considered a regionalist in the sense that his architecture is so sympathetic to the terrain and stresses simple and natural forms. Nevertheless, the sophistication of forms and shapes found in his structures reveal his training and learning. Appropriately in an era of pluralism and acceptance of many ways of building, Fay Jones has been recognized as a significant creative figure working quietly and consistently in the foothills of the Ozarks.

Robert Adams Ivy, Jr.'s Fay Jones (1992) offers a succinct discussion of the architect and a number of his works are beautifully illustrated. Included is a complete bibliography, which can direct the reader to numerous articles in such publications as House Beautiful, Architectural Digest, Progressive Architecture, Architectural Record, and L'Architettura. An article by Michael Ryan on the architect in Parade magazine (January 17, 1993) provides a good general introduction. Also, Robert T. Packard's Encyclopedia of American Architecture (2nd edition) (1995).