When the former Buffalo Bible Institute merged with Houghton College in 1969, the West Seneca campus was created.

The 1,300 acres (5.3 km2) of campus sit on the Allegheny Plateau at roughly 1,300 feet (400 m), on the site of the former Caneadea Indian Reservation.

East Meets West involves taking integrated classes during normal semester then traveling abroad during "May Term", exploring the roots of Western culture.

Science Honors takes place during both first-year semesters at Houghton, involving research in recent real-world issues such as fuel-efficiency, climate change, and energy sources.

[14] As part of this commitment, the school has built one of the largest solar arrays in the state of New York, with a ribbon cutting ceremony on April 17, 2015.

The Highlanders previously competed in the defunct American Mideast Conference of the National Association of Intercollegiate Athletics (NAIA) from 2001–02 to 2011–12.

Houghton's first national champion was Kaitlin Fadden who won the 2008 NAIA Outdoor Track and Field marathon event in a time of 2:57:10.

[17] In 2014, the university opened the Kerr-Pegula Athletic Complex thanks to a $12 million gift from 1991 graduate Kim Pegula.

[18] The complex is named after Kim's father Ralph Kerr, an instructor in Houghton's Adult Education program, and her husband Terrence Pegula.

Three lighted turf facilities are home to the Houghton Highlander soccer, baseball, softball, field hockey, and outdoor track.

It also provides dedicated practice space for outdoor sports over the winter and during inclement weather and serves as a hub of involvement for the campus and the surrounding communities of Northern Allegany County and Western New York.