In 1938, a small group of Protestant families living in the rural community of La Mesa, then located on the eastern outskirts of Albuquerque, began gathering for Sunday school in the original La Mesa School, a one-room building at the corner of Louisiana Boulevard and Copper Avenue.  Rev. David Reiter, a Presbyterian minister serving with the Board of National Missions, helped organize the class and lead worship for approximately twenty adults and children.  The group became known as the La Mesa Community Sunday School. 

Two years later, when a four-room school was built at Copper and Española, the rapidly growing Sunday School class moved with it and continued to meet at La Mesa Elementary School until 1945.  Several denominations were interested in establishing a church in the community and sent delegations to have conversations with the class about affiliation.  A vote was taken and a decision made to become a Presbyterian congregation.  On November 9, 1942, eighty-three people signed a petition to the Rio Grande Presbytery requesting permission to organize a congregation.  Later that year, Rev. Morton Young was appointed as organizing pastor and on February 4, 1944, the La Mesa Community Presbyterian Church was formally organized with thirty-two charter members. 

In 1942, land at the northwest corner of Española and Copper was acquired with assistance from the Board of National Missions.  Using lumber salvaged from Civilian Conservation Corps barracks in the Jemez Mountains, the congregation erected its first church building on the site in 1945.   Rev. Young left in December of 1946 and was followed by short pastorates of Rev. D.  Lennington and Rev. Lane C.  Findley.  In 1948, the church called Rev. William Dalton to be its first full-time pastor.  The sanctuary was constructed during his tenure.  When he retired in 1950, the church called Rev. Harry Summers as pastor.  During his fourteen-year pastorate, church membership grew from 68 to more than 500. 

In 1964, after a fourteen-year tenure, Rev. Summers accepted a call to become the first Executive Secretary of the New Mexico Conference of Churches. A used pipe organ donated by Immanuel Presbyterian Church was installed in the sanctuary in 1965. Rev. Stewart Coffman was installed in 1966. A bell purchased from a congregation in Missouri was added to the bell tower in 1967.  Rev. Coffman left La Mesa in 1969.  Rev. Gary J. Looman began serving as pastor in 1969 and remained until the spring of 1978.  The church expanded its ecumenical work and adult Bible study during his pastorate.

Rev. Howard Paul was installed as pastor in January 1979.  Under his leadership, La Mesa became more involved in the neighboring community and in work with the Presbytery of Santa Fe and the Synod of the Southwest.  He helped organize a celebration of the 50th anniversary of the church in February of 1994.  One of the most significant decisions during Rev. Paul's ministry came in the late 1980s when the congregation undertook a process of discernment about its future.  Members considered relocating to another part of Albuquerque but ultimately chose to remain in the La Mesa neighborhood and deepen their commitment to the surrounding community.  That decision led to a major expansion of the church campus.  Groundbreaking took place in May 1994, resulting in the construction of a new Fellowship Hall, expanded office space, a parlor and library, and a commercial kitchen. 

Rev. Paul retired in November of 1994 after a 15-year pastorate.  Rev. Bill Scholes was interim pastor and helped in the transition of moving into the new facility.  In March of 1996, Reverends Richard and Kathryn Pyke were called to serve as co-pastors.  They brought new energy to the programs and worship of the church.  They concluded their service in the fall of 1998. 

Rev. Trey Hammond began his pastorate at La Mesa in October of 1999.  He had been serving as the Coordinator for Urban Ministry of the national staff of the Presbyterian Church (USA), following 15 years of service in urban churches in the Dallas area. During his twenty-one years of ministry, the church deepened its connections with the surrounding community and expanded partnerships that continue to shape La Mesa's mission today.

During the early twenty-first century, La Mesa continued to strengthen its commitment to community engagement and outreach.  The congregation played a leadership role in Albuquerque Interfaith and helped support the founding of the Albuquerque Opportunity Center, a shelter and support program for men experiencing homelessness, in 2004.

In 2006, La Mesa launched the La Mesa Arts Academy in partnership with La Mesa Elementary School, providing free after-school instruction in visual arts, music, dance, and drama.  A major renovation of the church campus followed in 2012, including extensive improvements to the Learning Center and restoration work on the church organ.

Continuing its commitment to neighborhood partnerships, the congregation celebrated the groundbreaking of the La Mesa Neighborhood Garden Park in 2013.  These efforts reflected the church's long-standing dedication to serving both its congregation and the broader community.

Following the retirement of Rev. Trey Hammond in 2020, the congregation entered a period of transition.  In 2023, Rev. Dr.  Brett Mitchell was called and installed as pastor, continuing La Mesa Presbyterian Church's tradition of worship, service, and community engagement.

From its beginnings as a Sunday school class meeting in a one-room schoolhouse in 1938, La Mesa Presbyterian Church has grown into a vibrant congregation committed to worship, learning, service, and community partnership.  Throughout its history, the church has sought to respond faithfully to the needs of its neighborhood while remaining rooted in the Presbyterian tradition.  Today, that commitment continues as La Mesa serves both its members and the wider Albuquerque community.