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The idea of establishing a Catholic high school originated from the mind of Fr. Espiritu Hizon, parish priest of Bacoor from 1951 to 1955. However, this was not realized because he was transferred to another parish. Fr. Eliseo Peregrino took over his post and made the necessary preparation for the creation of the school. He met some leaders of the parish and proposed the holding of a fundraising project "Queen of May." The proceeds of this contest were used for the construction and purchase of the furniture of the school.

In July 1951, St. Michael's Institute formally opened its door to fourteen students. Mrs. Angelica Rito served as the principal with the following as teachers: Fr. Eliseo Peregrino, Religion; Mrs. Angelica Rito, English; Miss Virgilia Velasquez, Science; Miss Visitacion dela Cruz, Math; Miss Ybadlit, Filipino and Miss Felisa Cuenca, Vocational. Miss Emilia Tortona later came in as a Filipino teacher.

In 1958, Fr. Peregrino was given a new assignment in another province. A dynamic priest, Fr. Leon Coronel, assumed directorship of the school. In March 1960, the school had its first commencement exercises with 12 graduates. Violeta G Enriquez emerged as class Valedictorian, Alice Z. Pagusan, as Salutatorian, and Ernie Alcova as First Honorable Mention.

Meanwhile, new faces joined the faculty. Among them were Mr. Alejo Rubio, Mr. Antonio Villanueva, Mr. Luis Felizardo, Miss Rosales, Mrs. Lucia Villanueva, Mr. Manalili, Mr. Tayag, Miss Corazon Ercia, Miss Zenaida Danofra and others.

During the year 1965-66, Fr. Coronel introduced a new administrative structure. He invited the Sisters of Saint Zita under the Congregation of the Oblates of the Holy Spirit to administer the school. Sister Teresiana took over as the principal. The new religious administrators started the grade school department organizing the first kindergarten class and adding a new grade every year. After two years, Sister Teresiana was replaced by Sister Maria Piera.

In 1967, typhoon Welming destroyed the school. Classes were conducted inside the church so as not to interrupt the submitted school calendar. Fr. Coronel embarked on a new project, the construction of a new two-story school building. This new building was blessed on March 8, 1968, by His Excellency Msgr. Artemio G. Casas, Bishop of Imus.

The school year 1968-69 marked another change. The sisters of the Sacred Heart took over the administration of the school. Sister Mary Emmanuel acted as principal assisted by Sisters Mary Bernard and Mary Gertrude. Sister Maria Socorro was the Superior. It was during their supervision when the school had a rapid increase in enrollment.

In 1972, Fr. Eugenio Marcelo became the next school director. Sister Mary Teresita served as the new principal in 1974. She introduced a lot of educational innovations and from then on St. Michael's Institute progressed in its educational apostolate. Mr. Joseph Godio was assigned principal in 1978 after Sister Mary Teresita.

In 1980, Fr. Nicanor T. Victorino became the director of the school as the successor of Fr. Marcelo. He worked for the expansion of the high school building and additional rooms for the elementary department. He also spearheaded the construction of the gymnasium which became a venue for different occasions not only for the school but also for the people of Bacoor. Dr. Rosalia Guinto, the new principal, known for her rich educational experiences, restructured the school's academic program; supervised teachers in their everyday tasks; handled discipline when it was necessary. All these were supported by the two Assistant Principal, Mrs. Rosalinda C. Mendoza in the elementary and Mrs. Eugenia B. Blanco in the high school department.

The founding of St. Peregrine Institute, gave way for Dr. Rosalia Guinto to resign and leave St. Michael's Institute in 1982. Fr. Victorino hired a new principal, a retired public elementary school principal, Mrs. Araceli N. Ignacio from General Trias, Cavite. She worked seriously for the continuous improvement of the school. A Parents-Teachers’ Association (PTA) was organized and Mrs. Ignacio supervised and supported its projects. She gave Fr. Victorino an idea to put up a school canteen that was supervised by Mrs. Pacencia M. Camia. The income of the canteen became part of the school's financial stability. Mrs. Ignacio applied to the school for the accreditation of the Government Assistance to Students and Teachers in Private Education (GASTPE), a program of the government to subsidize the school fees of poor but deserving students. There were more improvements, renovations, constructions, and educational innovations during her term. Added to these, she continued her campaign for cleanliness and beautification of the school.

After 10 years of her commitment as the school principal, Mrs. Ignacio retired in March 1992. In June 1992, Miss Lina V. Bernal, a former Pastorelle Sister of Jesus Good Shepherd School in Imus became the new principal and served for one year.

In 1993, Miss Eugenia B. Blanco, an exemplary Physics teacher who also served as Assistant high school principal, was appointed as the new principal by the school board. It was Mrs. Amelia C. Loba who became the Assistant Principal of the high school department while Mrs. Rosalinda C. Mendoza remained as the Assistant Principal in the elementary department. Miss Blanco worked on the revision of the syllabi in all learning areas, restructured the co-curricular program of the school, and it is in her term when our school became a member of the Cavite Diocese Parochial Schools Association (CADIPSA) where teachers were sent to different seminars for their professional development.

Miss Blanco also encouraged teachers to enroll in graduate schools for future advancement in their teaching careers. Her tasks and responsibilities grew deeper and wider as she continuously and seriously performed them for the welfare of the entire school community.

On June 6, 2003, in line with the celebration of his golden sacerdotal anniversary, Fr. Victorino retired after 23 years of facing the challenges in his call of commitment as Director of SMI and as parish priest of St. Michael the Archangel Parish.

With the start of SY 2003-2004, the school welcomed a new director, Rev. Fr. Rosendo L. Ignacio. Fr. Endong (as everyone fondly called him) was a tireless priest from Sta. Maria, Bulacan but grew up here in Cavite. His plans for SMI favored both teachers and students. He wanted to raise the standard of SMI to make it more competitive and united under God's love. He nurtured the heart and mind of everyone for love to the Divine Mercy and St. Maria Faustina Kowalkska. As he continued being the director of SMI, the school continuously improved. Repairs, expansions, renovations, and re-paintings of school facilities were made.  Air-condition units were installed in the elementary rooms. The old elementary rooms on the 2nd floor in front of the school gate were renovated. Fr. Ignacio also initiated the Bible Enthronement in the school and for the teachers and students to read, meditate, and share the Gospel before the first period of class in the morning. He implemented the feeding program joined by Michaelians that was held once a week in selected slum areas in Bacoor.

After the untimely death of Fr. Ignacio, Fr. George Morales temporarily assumed the post and was appointed as OIC School Director from 2007-2009. He continued the unfinished projects of Fr. Ignacio with Fr. Teodoro Bawalan as the project engineer.

In 2008, the new three-story building was completed. It was temporarily blessed by Fr. Morales so it can be used for the opening of the school year 2008-2009. In the same year, the building was formally blessed by His Excellency Msgr. Luis Antonio G. Tagle, Bishop of Imus now Archbishop of Manila.

More changes had been made to SMI to provide the students the best learning environment. The school library was relocated to the second floor and became more comfortable due to the installation of an air-conditioned unit.

Fr. Morales was replaced by Rev. Fr. Teodoro Bawalan in the year 2009 as Director of SMI. Fr. Bawalan has been performing other tasks, being the Parish Priest of Our Lady of Fatima Parish Church in Binakayan, Kawit, Cavite. In two years, the dusty, rough, and rocky ground of the school was cemented, and corridors were covered with tiles. The old stage was demolished and replaced by a collapsible structure for the plan to construct a four-story building in preparation for the K to 12 Curriculum. In the school year 2012-2013, as part of the CADIPSA unifying system, SMI started an innovation for the computerization of the pupils and students' academic achievements, records, and data which was powered by a digital Information System and Technologies (DSAT).

In March 2013, the very hardworking and committed principal Miss Eugenia B. Blanco retired. Among the applicants, Mrs. Maria Lourdes Q. Narvaez, a very effective high school Math teacher was chosen by the Board of Directors as the new principal. The first achievement of Mrs. Narvaez, with the collaboration and cooperation of the entire SMI community, was the FAPE-ESC accreditation.

In the second year of Mrs. Narvaez as principal, SMI broadens its horizon with more improvements. LED projectors were installed in every classroom in the high school department, the implementation of E-Text ID system, the use of a new set of uniforms for the pre-elementary department and Grade VII, the installation of air condition unit in Grade VII, Grade IX, and Grade X classrooms. In addition, SMI also acquired the ownership of Scuola deli Angeli which was donated by the generous owner, Mr. Zosimo Angeles. The aforementioned school is now known as St. Michael’s Institute (Habay Branch) which currently offers Kinder to Grade III with Mrs. Soledad S. San Jose as its Academic Coordinator.

In the school year 2014-2015, an Administrative Council was established to promote better consultation and transparency on matters of school policies and management. Mrs. Narvaez desires to achieve academic excellence through her diplomatic and nurturing approach to involving the whole SMI community. She aims to continue the legacy of making SMI a deacon of quality learning by giving the students a truly evangelizing and transforming education thus preparing them to be more competitive and agents of social transformation.

In April 2018, everyone was shocked by the burning of the two-story building, which is considered the oldest building in the school. Alumni showed their love and care for their beloved school. Various aids abound; whether financially or ability to rebuild the school in the wake of the tragedy. On this occasion, the people of SMI have revived “Malasakitan” so that the school can continue to provide quality education to those in need.

In the third month of School Year 2018-2019, Mrs. Beatriz R. Miranda, school Registrar and a Religion teacher was appointed as the newest principal. In her first months of the administration, she showed a strong desire to increase and further improve the quality of school education. Currently, St. Michael's Institute is now a full-fledged school that provides concrete education from Kindergarten to Senior High School with a variety of strands: STEM, HUMSS, ABM, GAS, and ICT. Today, the school is achieving academic excellence towards shaping a student as a maka-Diyos, maka-Tao, maka-Kalikasan, at maka-Bansang individual.

Mrs. Miranda continues to lead along with the newly appointed Administrative Council from the year 2019 to the current year. The members of this Administrative Council are Ms. Maria Katrina DP. Palado, Coordinator of External Relations, Mrs. Linda Celestino, Coordinator of Physical Plant, Mr. Christian Joseph C. Vales, Coordinator of Christian Values ??Integration Office, Mr. Ralph Robert J. Alalay, Coordinator of Office for Student Affairs, Mr. Henestrel R. Tabinas, Coordinator of Office for Curriculum and Instruction - Senior High School, and Mrs. Soledad S. San Jose, Coordinator of Office for Curriculum and Instruction - Elementary and Junior High School and Assistant School Principal.

Unexpectedly the whole world experienced a pandemic in the current year. In this situation, many questions run through everyone's mind as to how students can continue their education even though many cannot leave home and gather together. In June, the Diocese of Imus Catholic Educational System Inc. implemented the project for catholic schools to continue the school year 2020 - 2021 despite the pandemic. Through Flexible Learning Program or FLEX St. Michael’s Institute was able to continuously deliver quality education. This is an effective way to not interrupt the education of students even if they only stay indoors. With the collaboration of the school, parents, and students, the new way of learning became more effective and efficient.