In 1853, Father Andrew Bohan came from Holy Cross in Flatbush and celebrated Mass in a hotel on the northwest corner of Atlantic Avenue and Vermont Street. Father Bohan obtained six lots on the northwest corner of Atlantic and Van Siclen Avenues which were transferred to Bishop Loughlin. In 1954, the construction of a church was begun. On April 9, 1854, Bishop Loughlin dedicated it under the patronage of St. Malachy. The church cost $2,300 to build.
In April 1862, Rev. Patrick Creighton became the first resident pastor of the parish. He renovated the little frame church and established the first Catholic school in the town. Securing a three story building on Atlantic Avenue and nine adjoining lots, he opened his school in August of 1868.
In 1929 a catastrophic fire destroyed St. Malachy's school building. The heroism of the sisters during the fire won recognition from the secular press. Father Higgins, the pastor at the time, acquired the former Home for Orphan and Destitute Children, which had been a receiving and quarantine station. When the Home was relocated to Rockaway, Father Higgins converted the building into the parish school. Also, during his pastorate, Father Higgins had the wood frame church building reinforced with brick and concrete.
In 1939, the next pastor, Father Daniel P. Kane, renovated the entire school. He beautified the parish grounds with the creation of outdoor grottos in 1941. It was during this latter year that a kindergarten was opened. Within a few years, the school was renovated and running again.
In March 1957, Father Henry G. Doheny, the current pastor, announced an ambitious $200,000 building fund campaign to construct a new 12 classroom school and an adjoining parish auditorium capable of seating 800 persons. By the time the new school opened in 1958 with an enrollment of nearly 600 students, the building campaign had raised $245,000. In April 1968, a new Convent was opened. Because the response of the people was so great, there was no debt on the building.
The complexion of St. Malachy was rapidly changing. The older established families of German, Irish and Italian descent were moving to Queens, Nassau and Suffolk counties and were being replaced by Spanish speaking parishioners. Father McElroy instituted a Spanish Mass early in his pastorate.
With the population shift in the parish, St. Malachy's financial status became adversely affected to the extent that both the school and church required diocesan subsidies to maintain their existence. Father Raymond W. Kutner, was installed Administer or the parish on September 8, 1978. He immediately set upon the task of reviving St. Malachy financially. More difficult was the necessity of making an immediate decision about the future of St. Malachy's School. In a move to save quality Catholic education for the children of the area, a majority of the Cluster Coordinating Committee voted to close both St. Malachy and the neighboring St. Michael schools and to reopen a consolidated school operated by both parishes. The new school was called St. John Neumann School located on the site of the former St. Michael's High School on Jerome Street.
St. Michael's parish and St. Malachy's parish now form the Parish of St. Michael-St. Malachy. St. Michael's Church is the principal worship site.
On May 29, 2015, Bishop Nicholas DiMarzio sent a letter stating that the agreement the Diocese had with the Fathers of the Institute of Incarnate Word to pastorally administer the parish for the previous 13 years had expired and would not be renewed. The pastoral administration of the parish was given back to the Capuchin Friars effective on June 30, 2015.