What is known as Trece Martires City used to be Quintana. This was the largest, most remote and one of the oldest barrios of Tanza, Cavite. In the early 19th century, settlers from Indang, Amadeo, General Trias and Tanza and from nearby Batangas province came to inhabit Quintana.  The first known settlers were the Arias, Asas, Erni, Ferrer, Lubigan, Salazar and Villalobos families.  The whole barrio of Quintana was a friar land of the Santa Cruz de Malabon Estate.

From 1900-1930, the place was subdivided into cattle ranches and sugar farms owned by the Valencia and Soriano families of Tanza. Just before the outbreak of World War II, the government awarded these lands to the tenant-occupants on an installment basis. From settlement period to 1940's, the educational aspect of life was greatly overlooked and neglected by the government and barrio leadership until the first public school was opened in a rented house where the first teacher was Emiliano Bobadilla; Miss Lucia Sosa succeeded him until the outbreak of World War II in December 1941. The second school was re-opened in 1945 with Mr. Gelacio de Padua as the teacher.  Mrs. Victoria R. Lubigan then succeeded him. When she was transferred to Amadeo, the school was closed for lack of teacher. 

From 1945 to 1953, the place was continued to be the wild rendezvous of lawless elements and wanted criminals, because of its distance and absence of transportation and communication facilities.  Because of this situation, the people became frustrated and many of them left the place.  The assumption to the Presidency of Ramon Magsaysay changed the events of life.  The people who had transferred elsewhere have returned to their homes and fields.

The Charter of the City was done through the efforts of several respected lawmen from Cavite, which started from the vision of Senator Justiniano, Congressman Jose T. Cajulis who authored House Bill 1795 and became Republic Act No. 981, in May 24, 1954 when President Ramon Magsaysay signed it into law.  Under this charter, the Governor of Cavite will serve as Ex-Officio City Mayor of the city. 
The city was named in honor of the Thirteen (13) Martyrs of Cavite, who were sentenced to death during the Spanish Regime. These were: Antonio San Agustin (Quintana II), Alfonso de Ocampo (Quintana I), Victoriano Luciano (Bitangan), Severino Lapidario (Bayog), Luis Aguado (Fiscal Mundo), Eugenio Cabezas (Palawit), Feliciano Cabuco (Kanggahan), Hugo Perez (Lukbanan), Jose Lallana (Panuka Gubat), Maximo Gregorio (Aliang), Maximo Inocencio (Bagong Pook) Francisco Osorio (Project) and Agapito Conchu (Lagundian).  These also became the names of the Thirteen (13) barangays in the city.

Trece Martires City was inaugurated as Provincial Capital on January 1, 1956, on the same day Governor Montano was sworn into office as Cavite's Provincial Governor and Trece Martires City's Ex-Officio City Mayor. He "inherited" it from its First Ex-Officio City Mayor, Acting Governor Dominador Mangubat, when it was barely one year old.  When his term expired in 1971, the new city was pretty well in its teens (17), the capitol standing in the solitary grandeur and lording it over a vast area, its territorial limits extending "ten kilometers from its heart in all direction of the compass".

Trece Martires City became the Provincial Capital, it is interesting to note, in three stages. First, under Republic Act No. 981 the new city comprised a territory not exceeding one thousand hectares, located at or near the intersection of the Tanza-Indang Road and the Naic-Dasmariñas Road in the Province of Cavite.

Second, on June 22, 1957 the original act was amended by Republic Act 1912 increasing its territory to 3,917 hectares.  Consequently, the Municipalities of Indang and General Trias had to yield parts of their respective areas to this territorial expansion.
Finally on April 7, 1959 Republic Act 2139 was approved by the Congress of the Philippines giving Trece Martires City administrative jurisdiction over a 100-meter strip of land along and including four national roads radiating from the city to Tanza, Indang, Matanda and Tres Cruces Dams, thus stretching the territorial limits by ten kilometers all around.

Governor Montano chose to hold his inauguration as Cavite's Provincial Governor and Ex-Officio City Mayor of Trece Martires City on January 1, 1956, coinciding with inauguration also of the new Provincial Capitol. This double inauguration served to emphasize the significance of the birth of the third and newest City of Cavite from which radiated the highest political and administrative power and influence in the province.  That the city was named after the thirteen Caviteños who were executed by the Spaniards shortly after the outbreak of the Philippine Revolution is indicative of the message that the people of the province hope and expect it to carry out-a message of redemption from bondage to freedom and prosperity.

To date, Trece Martires City had six (6) Ex-Officio City Mayors, namely, (1) Dominador Mangubat (1954); (2) Delfin N. Montano (1956-1971); (3) Lino D. Bocalan (January 1-Septemebr 30, 1972); (4) Dominador M. Camerino (October 1, 1972-July 25, 1979); (5) Juanito R. Remulla (September 25, 1979-May 1986); (6) Fernando C. Campos (May 1986-January 1988) and (7) Juanito R. Remulla (February 1988-May 1992).

On June 11, 1977, then President Ferdinand E. Marcos signed Presidential Decree No. 1163 relocating the capital and seat of government from Trece Martires to City (then-municipality) of Imus. Governor Juanito Remulla requested Marcos in September 1979 to transfer the capital back to Trece Martires City. As of 2011, the provincial capital is still Imus City, but most of the provincial offices are still located in Trece Martires City. Thus, making Trece Martires as a de facto capital of the province, while Imus as a de jure provincial capital.[10]
There was an attempt made in January 1988, to elect the local officials to run the affairs of the city government and ease the burden of the Ex-Officio City Officials but it was denied by the Supreme Court Resolution dated January 12, 1988.

On March 31, 1992, the Republic Act no. 7325 was approved by President Corazon C. Aquino amending the charter of Trece Martires City, allowing the city to vote their own local officials for the first time.

Finally on May 11, 1992 the first local election was held per Republic Act 7325, an "Act providing local elections of the City of Trece Martires." The act is a consolidation of House Bill No. 3509 and Senate Bill No. 1938 amending the City Charter.  This was passed by both houses on February 5, 1992 and February 4, 1992 respectively and was signed into law by the President, Her Excellency Corazon C. Aquino on March 31, 1992.

The first elected city officials were: Mayor Prudencio M. Panganiban, Vice Mayor Remigio L. de Sagun, City Councilors-Eufrocia C. Roguel, Verixcio Amparo, Jose C. Villa, Luis S. Colada, Alfredo A. Sierra, Rolando Lontoc, Antonio Lubigan, Lamberto Lubigan, Pedro Marquez and Larry V. Adelante. Ex-Officio Members of the City Council are ABC President Emilio P. Colorado Sr., and SK Federation President Emelinda Amparo.

From the old annex buildings of the Provincial Capitol known as Ciudad Bulwagan, the administration building of the city was transferred on November 12, 1998 to the newly constructed City Hall located in 12,972 square meters of lot near St. Jude Thaddeus Church.
The second elected Local Chief Executive is Hon. Melencio L. de Sagun Jr. whose vision is to transform the city not only as the City of Sampaguita but also as a city with clean human resources by eradicating illegal gambling. Also being the capital and located at the heart of the province, the city houses not only the provincial government but also several national government agencies making the city the seat of local and national government and functioning as the administrative center of the province.

To date, the third elected City Mayor is Hon. Melandres G. De Sagun, a former SK Federation President, former ABC Federation President, son of former Mayor Jun Sagun and historically the Youngest Elected City Mayor in the entire Philippines. His platform of governance is Moving Directly to Success and the transformation of the city into " City within the Woods".