In May, 1937 four Sisters - Sister Dolorata, Sister Lourdes, Sister Marista and Sister Vianette - came all the way from Manila in response to the challenge put forth to the SSpS Congregation by the late Archbishop of Manila, Most Rev. Michael O. Doherty, DD, to extend its educational apostolate in Bulacan, making Malolos its base for the congregation's school ministry. To the four fell the challenge of laying the foundations of Immaculata Academy. Sister Dolorata was named superior-principal of the community and the elementary school that was already existing as a parochial school in Malolos since 1919.

The house of Don Antonio Bautista at Pariancillo Street became the first building that housed the Sisters' cloister and the Grade 5 and 6 classrooms. The others (Grades 1-4) were located at the Tantoco house across the General Torres Plaza. The following year, 1938, the primary grades were moved to the Jacinto building near the Bautista house. Up to early 1940, the Sisters conducted their mission at the two houses, this time with the High School department already in operation.

The need for a permanent site for IAM was uppermost in the mind of the Sisters. It was a problem theat called for immediate solution. The Sisters entered into a lease contract with the Malolos parish priest, the late Fr. Enrique Reyes, allowing the use of the vacant lot on the right wing of the church's site for the proposed building of IAM. With the help of Dr. Luis Santos, a known Malolos philanthropist and benefactor, the new edifice joined Malolos skyline in 1940. By 1941, IAM's kindergarten, elementary, and high school departments were inside one ground.In 1947, the plan to create a boys' high school department came to the fore. The proposal materialized only in 1950. However, it was gradually phased out in 1965 until the chool graduated the last batch in 1968.

In 1980, a piece of land in Sta. Isabel, Malolos was purchased by the congregation. This was IAM's future site and the answer to the needs of a broader educational apostolate in the province. Gradually, it was developed and in 1986, the HS building and a covered court were put up. Thus, the HS department moved to the new site in June, 1986. A few years later, the Preparatory, elementary, and administration buildings were constructed. In June, 1989, the elementary department joined the HS department in the new school site; meanshile, the Prep pupils stayed in the former school building. In February 3, 1990 the Preparatory, Elementary and Administration building were blessed. In the same year, Immaculata Academy assumed its new name: Holy Spirit Academy of Malolos.

In June, 1998, the High School Department started to accept male students.

This is Holy Spirit Academy of Malolos - a school committed to the formation of the Christian Filipino who mut meet the challenges of his/her age... a school where a Catholic atmosphere permeates in the spirit of TRUTH in LOVE.