Since its founding, the university main controversies revolved around student satisfaction, recruitment and treatment of staff and faculty. Further, local communities allegedly felt discriminated against, marginalised and excluded. The backlash from students and local communities against the university prompted the university president then, Dr. Al-shiah, to speak out in 2016. He described the reports as rumors and lies against a university committed to institutional reform.
Students' Satisfaction In the past ten years, Shaqra University has received negative media coverage and backlash on social media in regard to its low levels of satisfaction among students. The most recent controversy happened in 2018 during an "open meeting" between the rector, Awad Al-asmary and a group of medical students. In the meeting, a medical student expressed his concern about the absence of Saudi nationals from the teaching staff body. In response, the rector accused the student of racism against non-Saudi academics in the university. The video, which was circulated widely on social media, caused a major backlash. The video recording of this meeting went viral and spurred the publication of op-ed pieces tackling the absence of professors of Saudi nationality. In 2020, students have also complained about the size of the classes as the university put classes caps at 90 students.
Faculty Recruitment and Alleged Cases of Nepotism In terms of controversies related to its recruitment of staff, such issues have been reported by several local news outlets. On several occasions, unqualified staff has been allegedly appointed because of their "connections" with high level officials. In 2015, Sabq, a Saudi news website, reported that an unqualified member of staff has been appointed based on the "recommendations" of a member of the Saudi Shura.
Jordanian Professors Dispute 2016 In 2016, a dispute came to the fore between a group of contracted Jordanian professors and Shaqra university. The dispute arose after the university signed employment contracts with the professors in Jordan but at a later date did not abide by its agreement. The Jordanian professors took legal action against the university for a
breach of contract. The case was settled out of court upon receiving financial compensation.
600 Security Staff and Unpaid Salaries In 2015, 600 security staff made official complaints regarding three months worth of unpaid salaries. The university denied responsibility claiming that the security staff weren't employees of the university, but rather contracted to work for a security company. The security company in turn claimed the reason is due to late due payments from the university.
Staff absenteeism and Pay Deductions In September 2025, the Saudi media outlet, Sabq, reported on unauthorised absenteeism among staff in the university. In response, the university announced a number of measures to tackle an authorised absenteeism after summer breaks, including tracking employees attendance through in person sign-in sheets. Sabq also reported on dissatisfaction among staff after pay deduction in cases of authorised or an authorised absenteeism. Rather than a deduction of a full-day pay, staff demanded a deduction of only hours of absence. ==Claims of Exclusion and Marginalisation of Local Communities==