Javier Nepomuceno, the founder's first son convinced Mr. Ricardo Flores to apply for a government permit to open a College of Commerce. It was he who designed a three-year diploma course following the De La Salle curriculum where he graduated. He also was one of the first group of instructors and became its first Dean. By 1950, he requested his friend and cousin-in-law, Carlos T. Valdes, who was then teaching at De La Salle, to teach auditing every Saturday at Holy Angel. The pioneer graduates numbering 23 received their diplomas in 1951. Thus making the College of Commerce the first full college established at Holy Angel.

In 1965, the graduates of that school year achieved a 100% passing rate in the Certified Public Accountant (CPA) board exam. The next two decades saw the growth of the college. It has grown to be the biggest college of the University because of the growing need of the commercial establishments in Angeles, which became a city in 1964. Despite the natural upheavals, the faculty strike in 1968, the declaration of Martial Law in 1972, and the offering of new courses and colleges, the College of Commerce has continued to grow through the years.

In 1989-90, the college adopted a new acronym, CBA, meaning College of Business and Accountancy. In the next school year, the government granted recognition to BSA.

The Philippine Association of Accredited Schools, Colleges and Universities (PAASCU) granted Level I accredited status to the college in 1993.

Additional courses in 1994 were Bachelor of Science in Accountancy (BSA) and Bachelor of Science in Business Administration (BSBA) major in Management/Entrepreneurship.

In 1995, PAASCU granted Level II accredited statuses to the college. This year, new and upgraded curricular programs marked the quest of the University for academic excellence. The BSBA program added Hotel and Restaurant Management Program (HRM), Management Information System (MIS), and Tourism as areas of specialization.

In 1997, the college absorbed the College of Secretarial Education. In the same year also, the college started round-table conferences with businesses, industries, government, and banking sectors. This year also marked the construction of St. Therese of Lisieux (STL) building to house the college. Its inauguration took place the next year, with Javier Nepomuceno as guest of honor.

In 1999, PAASCU granted Level II reaccredited status (conditional) to the college.

PAASCU granted Level II reaccredited status (clean accreditation) to the college in 2005. In December of the same year, the same accrediting body conferred Level III status to Accountancy and Business Administration.

In 2006, the Hospitality Management Program also attained Level I accreditation status through PAASCU.

In December 2007, the Commission on Higher Education (CHED) declared the Business Administration program as a Center of Development (COD); and in 2008, the International Assembly for Collegiate Business Education (IACBE) accredited all business and business related degree programs of Holy Angel University (HAU), the first in the Philippines and the Far East.

During the school year 2009-2010, a new course major, Legal Management, under BSBA was offered; while Hospitality Management is now a separate college.