With the Filipinization movement of the late 60's, the Filipino sisters assumed the leadership of the Philippine Franciscan Congregation and of St. Joseph's College, Q.C. from the Dutch pioneers. The vision and mission of the school was restated to reflect its deep concern over the changed political and economic conditions of the period and its commitment to quality education for social transformation, for service to the underprivileged and marginalized. The 70's and the 80's, amidst the challenges of martial law, social unrest and poverty, saw St. Joseph's College, Q.C. rise to the demands of socially oriented education: a tuition-free evening high school for urban poor youths, a grant-in-aid program to train professionals in education and social work for disadvantaged communities all over the country, development programs and projects in rural and urban poor communities (literacy, day care, community theatre), exposure-immersion programs in the curriculum. At the same time, excellence in education continued to be a key priority. PAASCU accreditation and re-accreditation of the liberal arts, education, social work and commerce programs were sustained and subsequently granted level 3 status. The graduates' performance in the social work and the education board exams were marked by 100% passing rates. The grade school was first accredited in 1981 and the high school in 1984. Both departments have undergone and gained re-accreditation since then.
The graduate school was opened in 1979 to specialize in education and staff development.
In recognition of its over-all performance as an educational institution, in 2001 the Commission on Higher Education (CHED) granted full autonomy to the College of Arts and Sciences, "for meritorious achievement in higher education in the provision of instruction and in the conduct of research and community extension service; for high performance of graduates in licensure examinations; and for maintaining a tradition of integrity and an untarnished reputation in the education service."
In 2007, the CHED once more granted full autonomy status to the College of Arts and Sciences.