The history of Barasoain Church also became the history of the Philippines. After General Emilio Aguinaldo transferred the capital of the Revolutionary Government in Malolos, a national convention was held on 15 September 1898 to write the Constitution in Barasoain Church. According to witnesses of the historical event, the opening day is glamourous. The houses along the procession route, now called Paseo del Congreso, are filled with colorful decorations with palmera leaves and flags. One hundred and ninety three delegates that represented each provinces of the Philippines like Fr. Gregorio Aglipay, Felipe Calderon, Antonio Luna and Teodoro Sandiko. Pedro Paterno was elected as the president of the convention. While the constitution is being written, in 29 September 1898, in this church, the independence of the Philippines was ratified that was announced in Kawit, Cavite in 12 June 1898.

On 21 January 1899, after a heated debate, the constitution was ratified. The republic was inaugurated on 23 January 1899 with General Emilio Aguinaldo taking oath as its first president. However, it lasted only for two years but it became the voice of the desire of the great Filipinos for independence, with their own government and own with its own flag waving. And, Barasoain Church, though as a religious institution built to worship God also became the place that announced the independence of the country. This is the reason why it is called the Cradle of Freedom and Shrine of Democracy.

 On 19 October 1898, a law was passed that was ratified by the congress to create the Universidad Literaria y Cientifica de Filipinas in the convent of Barasoain. Don Mariano Crisostomo was the secretary. This is also where the Instituto Burgos was located. Unfortunately, the university was dissolved as soon as American forces entered Malolos.

 On 1 August 1973, through the Presidential Decree No. 260, Barasoain Church was declared as a National Shrine. It provided for the maintenance and improvements of the shrine because of its colorful and important role in the history of the country. In the present, and in the future, people are assured of a neat and maintained place to see that became a silent witness to time when the Filipinos desired and moved to create an independent nation.​