[3] From the early 1990s,[4][5][6][7] St. Augustine's began to be challenged by legal problems, significant declines in enrollment, low graduation rates, and financial shortfalls,[4][6] all of which seriously threatened the institution by the 2010s.

[12] The first classes were held at the state fairgrounds in a former army barrack donated by Major General Oliver Otis Howard, the head of the Freedmen's Bureau.

[12] On October 18, 1896, the St. Agnes' Hospital and Training School for Nurses opened, becoming one of the primary Black healthcare facilities between Richmond and Atlanta.

[12] In 1947, Harold Leonard Trigg became the first Black president of St. Augustine's and oversaw an expansion of the curriculum and the college facilities, including the completion of Pennick Science Hall in 1952.

Under Boyer, St. Augustine's enrollment doubled, several new buildings, including the Emery Health Center, were built, and the curriculum further shifted from that of a normal college to a predominantly liberal arts focus.

Robinson retired in March 1995, and was praised by the college's board of trustees for his leadership, which had earned St. Augustine's "an international reputation for quality education and public service of an unprecedented order.

[22] Since the 1990s,[4][5][6][7] St. Augustine's has experienced increasingly serious financial problems, which along with administrative instability and other controversies have severely challenged the institution in recent years.

[26] In its notice placing the institution on probation, SACSCOC cited St. Augustine's for high indebtedness, failing to collect payments it was owed, and for excessive reliance on lines of credit.

[39] In April, amidst what The Chronicle of Higher Education characterized as "significant turmoil" and Diverse: Issues in Higher Education described as "financial problems...stemming from a loss in enrollment and revenue", the institution's board of trustees fired president Dianne Suber one month prior to her planned retirement, after nearly 15 years of leading the university.

[23] In July 2019, together with the former athletics director, acclaimed track and field coach George Williams, the university's former general counsel Kyle Brazile, and the former facilities and construction manager Clarence King, all of whom had been fired around the same time, former interim president Gaddis Faulcon filed a wrongful termination lawsuit against St. Augustine's.

Feggins subsequently filed a wrongful termination lawsuit against St. Augustine's, alleging retaliation, intimidation, and the institution's deliberate neglect of its student athletes, including refusing to provide adequate healthcare, meals, and insurance coverage for its football players.

"[42] On December 3, 2023, St. Augustine's reached crisis point when the SACSCOC voted to rescind the institution's accreditation for continued governance and financial management issues.

[45][46] The following month, local media reported the college was failing to pay all of its employees, with some faculty members unilaterally cancelling their classes until they received paychecks.

[49] According to interim president Burgess, the university was able to account for $10 million previously reported as unsupported by contacting vendors and creditors.

[9] On March 1, university officials said they would submit the matter to arbitration, followed by further litigation if necessary; until the conclusion of legal proceedings, St. Augustine's would remain accredited on probation.

[51] Interim president Burgess subsequently stated the institution was also pursuing accreditation through the Transnational Association of Christian Colleges and Schools (TRACS).

[59] According to the terms of the initial loan, scheduled to come due in 2025, $3 million was earmarked for past due and future payroll and taxes, $1.8 million for payments to the U.S. Department of Education, $650,000 for completing overdue financial audits for the 2022 and 2023 fiscal years, $600,000 for student refunds, $545,000 for property insurance, $375,000 for fees, title insurance and expenses, and $30,000 for appraisals.

"[60] After a delayed opening on September 3, due to the need to conduct maintenance to campus buildings, St. Augustine's began the 2024–2025 academic year with a diminished enrollment of 200 students.

[1] That month, Wake County Superior Court Judge James F. Ammons Jr. ruled FieldTurf USA could recover unpaid bills for installing artificial turf on a St. Augustine's football field by placing a lien on university property.

[61] Due to doubts about the university's ability to remain in compliance with their requirements, on October 4 the CIAA suspended all St. Augustine's athletics teams from conference competition for the remainder of the academic year, with immediate effect.

[63] In early November, the university reported completion of two overdue audits for the 2022 and 2023 fiscal years; among other issues, the audits revealed inaccurate accounting, a lack of oversight concerning financial reporting and major transactions, inappropriate procurement and approval procedures for "certain significant contracts," and that as of November 8, the university had unpaid payroll withholdings and taxes outstanding "of approximately $8.4 million, excluding interest and penalties.

[65] On November 14, a judge dismissed a lawsuit filed on May 31 by "Save SAU," a coalition of university alumni and supporters suing to remove the university's board of trustees for alleged financial mismanagement, and alleging Brian Boulware, as board chairman, had benefited from loan brokerage fees and had permitted large wire transfers without documentation.

Judge Becky Holt ruled the coalition lacked standing under state law to file suit against a nonprofit institution.

[3] The proposed agreement and any associated transfers of funds were placed on hold pending the decision of the North Carolina attorney general, whose office is required to review and approve any such transactions involving nonprofits.

[69] On December 10, SACSCOC again voted to remove St. Augustine's University from membership, as its Committee on Compliance and Reports found the institution remained non-compliant with six core requirements and standards, and had also reached the end of its maximum allowable probation period.

[73] On January 27, the North Carolina attorney general's office rejected St. Augustine's proposed agreement with 50 Plus 1 Sports in its existing form.

[74] On February 3, interim president Burgess said the university would indefinitely continue fully remote instruction to address unspecified deferred maintenance issues.

[85] Saint Augustine's University was the nation's first historically black college to have its own on-campus commercial radio and television stations (WAUG 750 AM, WAUG-TV 8, and Time Warner cable channel 10).