St. Joseph’s School continued to graduate intellectually and morally upright pupils. Unfortunately, the school was disrupted by the Second World War in 1941. In 1946, after the liberation, St. Joseph's School resumed its operation. There was an increase in enrolment then. The school administration requested the Mary Immaculate Concepcion Sisters of Canada to help administer classes in the elementary department. The first batch of Grade 6 pupils graduated in 1922. The school saw the need for high school education. Through the hard labor and dedication of Fr. Renato Vernacht, CICM, together with the administration, the faculty and some parishioners, more rooms were constructed. Thus, the Boys High School Department began to operate. This development paved the way to renaming St. Joseph's School to St. Joseph's Academy, the school that we know today and now popularly identified with the Las Piñas Bamboo Organ. By 1949, Fr. Antonio Van Overweld, CICM, was the new head of the school. To cater to the girls, he decided to establish the boys and girls high school (COED) in the First Year Level only. However, the school could only accommodate the big number of students in one section. In 1950, for the second batch of First Year students, the boys were separated from the girls. The boys were transferred to St. Andrew's School of Parañaque. This explains why the first batch of sixteen (16) students who graduated in 1953 were all girls

Since then, the school continued to operate smoothly with a clear sense of direction and vision. There was an expansion of its physical structure. In the 1960’s, a three-storey building and a new gymnasium were built. This marked the beginning of a continuous expansion to meet the demands of a growing school population. From the time it was fully established as an institution of learning, it strived to attain its goals. Its concern for its parishioners did not just focus on the young and adolescents. The school has become sensitive to the needs of the adults who could not afford to attend regular classes in the high school. In 1969, St. Joseph’s Academy, in cooperation with St. Joseph Parish, the High School Evening Classes for Adults (H.E.F.A.) was established. 15 In the 1980’s, major changes in the different aspects took place. The buildings were transformed and patterned after the structural design of the Las Piñas Bamboo Organ Church. The Diamond Building, which at present houses the auditorium was built in 1991. Later, the school insignia was changed into one featuring the world famous Bamboo Organ. These we owe with all gratitude to the selfless efforts of Fr. Mark Lesage, CICM, who was then the parish priest of St. Joseph Parish and Fr. Leo Reiner, CICM.

When Msgr. Allen C. Aganon took over as Director in the year 2000, renovations, improvements, expansions and changes were made. Facilities like comfort rooms, canteens, clinic, library, including the faculty rooms and different offices were renovated and improved. To meet the demands of technology, photocopying machines, computers, internet, communication lines (telephones and facsimile machines) were made available. In the year 2001, the logo was changed into one that features the image of St. Joseph with the Child Jesus and bordered on top by the famous Bamboo Organ. The school uniform was changed from blue to green to conform with the colors attributed to St. Joseph. The Drum and Lyre Band was established to hone talents in music and to represent the school in various programs. In December 2002, the department of athletics, under Msgr. Jovito M. Mejino supported by the SJA Alumni Association, unveiled the school’s official athletic logo “Hammerheads”. 

Under the auspices of Msgr. Albert A. Venus and Fr. Enrico S. Salazar, School Year 2005-2006 swept off the record with numerous changes that occurred. One of these is the realization of the new building conceptualized by Msgr. Allen C. Aganon. The newly-built building is adjacent to the Diamond Building. This is a four-storey building which houses the canteen on the first floor. The high-tech Smart Room sits on the second floor. The Library occupies the third floor and the Science Laboratory is on the fourth floor. This is a major change after the construction of SJ Hall (formerly known as the SJA Gymnasium) in August 2004. The old High School Library in the Diamond Building was converted into classrooms, portion of it was allocated for the Publications Room and the Student Council Office.

Inspired by the newly-constructed modern Spanish architectural edifices, creative ideas conceived worth-noting succession of accomplishments from the School Director, Msgr. Albert A. Venus. In 2006-2007, the Sports field which has been the site of both the school’s and interschool’s activities was improved. The High School H.E. room was also built at the south wing area of the Sports field. For Msgr. Albert A. Venus, anything is possible with God’s will in His time. In 2007-2008, he thought of granting the less fortunate students education they truly deserve. Thus, High School Evening Classes for Adults (HEFA) at the Ascension of Our Lord Parish in partnership with its Parish Priest, Fr. Benjamin D. Molina Jr. (SJA’s former Assistant Director) was extended. Moreover, a crown to the school’s glory was the Children’s World Championship earned by the Las Piñas Boys Choir (LPBC) in Graz, Austria held in the same year.

As the school moves toward the achievement of its goals, the PAASCU application in 2008 is a realization. It was then in 2014 that the Grade School Department has been granted initial accreditation (Level I). An immense yet a gratifying task of providing education paved the way to open the Nursery level as an expansion of the Preschool Education in 2009-2010. It was also within that year that the G.S. and H.S. Computer Rooms were innovated. Building 5 that sheltered the Clinic, Grade Two, Preschool, and LPBC Rooms was demolished and constructed in November 2009. At present, it towers into a four-storey building dedicated to the late Jaime Cardinal L. Sin. 

We believe that quality education begins with quality instruction aided by quality facilities. Today, St. Joseph’s Academy continues to enhance its facilities and to respond to the call for quality education by developing and molding its youth who will undeniably serve as pillars of community development and of nation building. It dedicates its services to the parishioners of St. Joseph Parish and the nearby parishes of Las Piñas, Parañaque and Cavite. 

The three  succeeding school directors, Msgr. Mario Martinez, Fr. Fidel Fabile, and Fr. August Pulido, amply supported by the extended Josephian community, shared in the same vision and mission of the school, keeping the Catholic faith alive within and around the campus while taking the school community to new frontiers in 21st Century Learning.