Metro Dumaguete College, Inc. was founded by Mr. Wilfredo S. Manila and his wife Dr. Delma P. Manila. It started as an Internet Café rented at the Gemini Building, Real Street, Dumaguete City — established to "provide a decent livelihood for my relatives." Since Dr. Manila was still working as manager of Land Bank of the Philippines (Bacolod Branch) at the time, she appointed her sister and a niece to manage the café.

After months of operation, and in consultation with relatives and business associates, the Internet Café was converted into a 4-WD Computer Training Center and registered with TESDA. It offered short-term courses: 2-Mo. Basic Software Operations, 3-Mo. Computer Technician Course, and 2-Mo. Web-Page Design and Animation. As enrollment grew, the Center moved to a bigger location along Dr. V. Locsin Street, Dumaguete City.

Dr. Manila retired from Land Bank of the Philippines (Bacolod Branch) and took over full management of the Training Center. Not only a banker and financial management expert, she is also a lifelong educator who always believed in education as a "velocity accelerator that can trigger a positive change in the life of a person." As an educator, she began working to convert the Training Center into a full college.

The Training Center's Articles of Incorporation were amended and the institution was renamed Metro Dumaguete College (MDC) — registered as a private, non-stock, non-profit educational institution. The college moved to the 3rd Floor of the NORECO II Building on Real Street.

MDC applied for permits to operate three four-year ladderized programs: Bachelor of Science in Business Administration (BSBA), Computer Science (BSCS), and Information Technology (BSIT) — alongside non-degree courses in Accountancy, Mass Communication, and Call Center training.

In SY 2006–2007, MDC enrolled 395 students — 100 in regular four-year courses and 295 in short-term programs. MDC also applied for additional four-year programs: Bachelor of Arts Major in Communication, Political Science, Bachelor of Science in Tourism Management, and Bachelor of Science in Travel Management. Through prudent financial management, MDC acquired additional facilities, gave its teachers a decent pay, and charged the lowest tuition fee among private schools in Dumaguete City. By SY 2007–2008, enrollment grew to 461 (305 short-term, 156 four-year), and additional key personnel and instructors were hired to meet growing student needs.

The search for a bigger campus was realized when MDC successfully negotiated a lease agreement for what is now known as the MDC-Buñao Campus. Today it houses an administration building, a Computer Training Center, and a five-room school building for Short-Term and TESDA-funded Vocational-Technical Courses — as well as the Kinder Integrated Development School (KIDS), offering nursery and kindergarten courses.

At the NORECO II Campus, MDC opened an English as a Second Language Department offering English Language and Voice Lessons to Korean and other Asian and European students — expanding the school's reach internationally.

With the shift to K-12 in the Philippine education system, MDC was granted permits by the Department of Education to operate Grade 11 and 12 Senior High School programs — offering ABM, GAS, and TVL tracks.

MDC moved to its current 5,567 square meter campus at E.J. Blanco Drive Ext., Daro, Dumaguete City. Three newly-built, fully-furnished buildings welcomed 275 Senior High School students, 160 college students, and over 300 TESDA scholars — marking a new chapter in the school's growth.