The history of Holy Spirit Academy of Malolos stems way back from 1937. May of that year, 4 sisters - Sister Dolorata, Sister Lourdes Malabuyoc, Sister Marista and Sister Vianette - came all the way from Manila to extend the SSpS educational apostolate in Bulacan. Thus, they laid the foundations of Holy Spirit Academy of Malolos, then named Immaculata Academy. 

The house of Don Antonio Bautista in Pariancillo Street (now Sto. Niño Street) became the first building that housed the Sisters’ cloister and the Grades 5 and 6 classrooms. The Grades 1-4 classrooms were at the Tantoco house across the General Torres Plaza. In 1938, the primary grades were moved to the Jacinto building near the Bautista house. But the need for a permanent site for Immaculata Academy of Malolos was the sisters’ top priority. So they entered into a lease contract with the Malolos parish priest, the late Rev. Fr. Enrique Retes, allowing the use of the vacant lot in the right wing of the church’s site for the proposed building of IAM. 

In 1980, a piece of land in Sta. Isabel, Malolos was purchased by the Congregation. From then on, the buildings everyone knows of today were constructed. In 1990, Immaculata Academy of Malolos was renamed Holy Spirit Academy of Malolos.

The School voluntarily submitted to the PAASCU self-survey in the school years 2004-2005 and 2005-2006 for the elementary and high school departments respectively. The formal survey was conducted for the grade school in the school year 2005-2006 and 2006-2007 for the high school. The school received a three-year Level I Accredited Status. 

The school underwent the re-accreditation process in 2008-2009 for the elementary and high school respectively, thus resulting in a five-year Level II Re-Accredited Status. The same process would happen again in school year 2014-2015. 

In school year 2016-2017, the Mother Josepha Building, also known as the Senior High School building, was constructed in support of DepEd’s full implementation of the K to 12 Curriculum.

 In the same year, the school applied for PAASCU Level III Status, and fortunately, the institution had been granted such for both grade school and high school departments in May 2017. 

In the school year 2022-2023, the school was granted PAASCU Level III Re-Accreditation for five years.