The history of Texas A&M University–Commerce (A&M–Commerce) since 1996 comprises the history of East Texas A&M University since East Texas State University (ETSU) was renamed and admitted into the Texas A&M University System. In this period, A&M–Commerce has been led by four presidents: Jerry D. Morris, Keith D. McFarland, Dan R. Jones, and Ray M. Keck, and has seen the number of students increase from 7,400 in 2000 to 13,000 in 2015. A number of new buildings have been added since 1996, most notably the Morris Recreation Center (opened in 2003), the Keith D. McFarland Science Building (2006), the Rayburn Student Center (2009), and the Music Building (2011). In 2016, the university's Carnegie Classification was upgraded to "Doctoral University-Higher Research Activity" (R2), due in part to an Air Force Research Laboratory (AFRL) Summer Faculty Fellowship and Fulbright Scholarships awarded to its faculty.

A&M–Commerce has become increasingly diverse during this period, most notably in terms of Hispanic students, who have grown from approximately 7% of the student body in 2008 to about 18% in 2015, which has allowed the university to be designated an "emerging" Hispanic-serving institution (HSI) in 2014. A&M–Commerce has also created an Honors College, a related Regents' Scholars Program, and a nursing program since 1996. Additionally, the university collaborates with area junior colleges such as Eastfield College, Navarro College, Paris Junior College, and Tyler Junior College.

Transition to the Texas A&M University System

East Texas State University (ETSU) was renamed Texas A&M University–Commerce (A&M–Commerce) in 1996 when it joined the Texas A&M University System (TAMUS), during the tenure of President Jerry D. Morris. ETSU's main campus in Commerce was one of three institutions to join TAMUS that year, along with its branch campus in Texarkana (renamed Texas A&M University–Texarkana) and Baylor College of Dentistry in Dallas. In 2012, then-President Dan R. Jones credited joining TAMUS with accelerating the growth and beautification of the A&M–Commerce campus.

McFarland presidency

In 1998, graduate school dean Keith D. McFarland was named the 10th president in the history of A&M–Commerce. By 1999, the university was offering classes at its Metroplex Center in Mesquite, the Universities Center at Dallas (through the Federation of North Texas Area Universities), and at Navarro College in Corsicana, in addition to at its main campus. It also began holding commencement exercises in Corsicana in 2001, graduating over 2,000 students there by 2015. During the fall semester in 1999, the university counted 7,762 students and 235 faculty, and was divided into three colleges: the College of Arts and Sciences, the College of Business and Technology, and the College of Education. Total enrollment grew from 7,400 in 2000 to nearly 9,000 in 2007.

In 2002, a former A&M–Commerce cafeteria was repurposed and reopened as the Northeast Texas Children's Museum. In 2004, the university inaugurated a new Equine Program. A&M–Commerce founded the Bill Martin Jr Memorial Symposium in 2005, which honors children's author Bill Martin, Jr. and focuses on teaching reading to children. Since the inaugural event, its keynote speakers have included Brod Bagert, Gloria Houston, Steven Kellogg, Jerry Pallotta, Brian Pinkney, and Jane Yolen. In 2005, the university remodeled its Wathena Temple Home Economics Building into the Wathena Temple Fine Arts Building, as a replacement for the Creative Arts Village that had existed since the 1970s.

The National Science Foundation has supported research at A&M–Commerce with its Research Experiences for Undergraduates program since 2005, including a $300,000 award for chemistry research spanning from 2013 to 2016. The university opened a new science building in 2006, which is home to its Biology and Environmental Sciences, Chemistry, and Physics and Astronomy departments, as well as 29 research laboratories and an 87-seat planetarium. The planetarium hosted 28,000 visitors for its shows during the first year of its operation, nearly doubling its goal of 15,000 patrons for that year; by its second year, it had hosted over 60,000 people, the majority of whom were schoolchildren. In 2009, the planetarium celebrated the International Year of Astronomy by hosting a public observing night at the university's observatory and shows documenting Galileo and the history of the telescope.

Starting in 2006, A&M–Commerce has hosted the annual Cotton Belt Regional Railroad Symposium to document and preserve the history and legacy of the St. Louis Southwestern Railway, commonly referred to as the "Cotton Belt Route", and other former and current railroads in Arkansas, Louisiana, and Oklahoma as well as Texas. Also in 2006, musician and Fannin County native Ruby Allmond's music collection was donated to the university's James Gee Library by her longtime friend and musical collaborator, Audra Brock, after Allmond's death.

In 2007, A&M–Commerce established its Honors College, which provides full-ride scholarships, full fees, and free apartment housing for approximately 50 students each cohort. All Honors College students are required to maintain a grade point average (GPA) of 3.3 or higher, take 30 credit hours of honors-level courses, complete 96 hours of service, and successfully defend an honors thesis. The first cohort of 21 Honors College students graduated in May 2011. In fall 2010, the related Regents' Scholars Program was established, which annually awards 30 freshmen with a four-year scholarship that covers 70% of their tuition, fees, and room and board costs. The program emphasizes awareness of cultural and international issues, leadership, and traveling experiences.

In March 2007, A&M–Commerce library employees began conducting oral history interviews with area veterans of World War II, the Korean War, and the Vietnam War, collecting approximately 170 such interviews by July 2008. The resulting digital content was first made available to the public on Veterans Day in 2007, and by July 2008 25 oral history interviews could be accessed online from the library's website. Also during the 2007–08 academic year, the university demolished three former residential buildings: the Century House apartments, Hubbell Hall, and Mayo Hall, the latter two of which were men's dormitories.

In 2008, after broadcasting from the Performing Arts Center since 1977, campus radio station KETR moved into a new studio in Binnion Hall. In July of that year, the university announced needs-based $1,000 "Rising to the Challenge" scholarships for students at Grayson College, Navarro College, Paris Junior College, and the Eastfield campus of Trinity Valley Community College who were planning to transfer to A&M–Commerce. Also in 2008, President McFarland retired, although he later served as interim provost at Texas Woman's University in 2010 and then acting president of Texas A&M University–Texarkana in 2012. Also in 2012, A&M–Commerce renamed its science building as the Keith D. McFarland Science Building in his honor, which was formally marked with a renaming ceremony held in March 2013.

Jones presidency

In July 2008, Dan R. Jones was named the 11th president of A&M–Commerce after serving as provost and vice president at fellow TAMUS member Texas A&M International University in Laredo for the previous five years. When Jones began as president in Commerce in 2008, Hispanic enrollment was approximately at 7% of the student body, although during his tenure it rose markedly, to about 18% by fall 2015. In spring 2009, the university created an Office of Hispanic Outreach as part of its efforts to become a Hispanic-serving institution (HSI). By spring 2014, it gained "emerging" HSI status as its full-time equivalent enrollment for Hispanic students surpassed 15%. In his first address to the university community in August 2008, Jones outlined three of his initiatives for demonstrating the value of the institution: strengthening "the link between strategic planning and the budget", implementing a "strategic enrollment management team", and focusing on service, both "to students and to one another".

In 2009, the university opened a student services-oriented "One Stop Shop" and a new student union, named the Rayburn Student Center after alumnus Sam Rayburn, which was expanded by in 2014. By 2010, the growing university had an additional campus in Midlothian and also held classes at the Collin County Community College District and Northeast Texas Community College, in addition to in McKinney. That year also marked the inaugural Block Party, a concert for students held at the beginning of the fall semester. The university additionally purchased and began operating the Twin Oaks Blueberry Farm, which is located south of campus in Campbell, in 2010. Also in 2010, A&M–Commerce's Children's Learning Center, which provides on-campus child care for parents who are students, staff, or faculty at the university, was awarded the prestigious "Texas Rising Star" distinction for "exceeding state licensing requirements". Additionally that calendar year, the university created the African American Male Mentor Program (AAMMP), which has the goal of providing its participants "with a rich, well-rounded university experience while strengthening their confidence, academic abilities, and self-esteem".

During the 2010–11 academic year, A&M–Commerce produced more teachers than any other university in TAMUS. By 2010, the university's enrollment exceeded 10,000 for the first time in its history. In 2011, enrollment eclipsed 11,000, and in 2012 it surpassed 12,000. In fall 2014, the trend continued as the university's enrollment set an all-time record at 12,321, while during fall 2015, it broke the 13,000-student mark for the first time.

In 2011, A&M–Commerce opened a new Music Building at a cost of $29 million that features a concert hall able to accommodate 600 people as well as a 75-seat recital hall and five rehearsal halls. That year the university also opened a then-unnamed, three-story residence hall (later christened Pride Rock), which cost $14 million to build and can house 258 students. Additionally, Fulbright Scholarships were awarded to history professor William Kuracina in 2011 (for conducting research in India), to Curriculum and Instruction doctoral student Diana L. Hopes in 2013 (Guatemala), and physics and astronomy professor Carlos Bertulani in 2015 (Brazil).

In 2012, A&M–Commerce's Wind Ensemble and Chorale performed in a show called "Deep in the HeART of Texas" at Carnegie Hall in New York City. Also in 2012, 44% of the university's operating budget was provided by tuition and fees, 32% by state appropriations, and the remaining 24% via other means. In October of that year, the university joined the Southeastern Association for Research in Astronomy consortium. New degrees and programs created by the university that year included a Bachelor of Science in Nursing degree program (which would be accredited by the Commission on Collegiate Nursing Education in December 2014) and an entirely online Master's of Science degree in biological science. A&M–Commerce also opened an off-campus instructional site in Rockwall in 2012, which the university announced would be closed in 2017 due largely to low enrollment. The university also began a credit-transfer partnership with Paris Junior College in 2012, and then secured similar partnerships with Tyler Junior College in 2013 and Navarro College as well as Eastfield College in 2015. In addition, the university built an amphitheater in 2012.