Adonay is the eldest of the 11 children born to farmers Mariano Adonay and Prudencia Quiteria in the town of Pakil, Laguna in the Philippines, then under the colonial rule of the Spanish Empire. The exact date of his birth is unknown but official documents indicated his baptismal date to be on February 6, 1848, and has been recognized as his de facto birth date. However, researchers suggested that baptism in the town at that time was generally performed within a day after birth, making February 5, 1848 as his probable date of birth.
His father, aside from being a farmer, also played wind and brass instruments as a member of one of the town bands. Adonay in his early childhood showed enthusiasm for his father's musical instruments. As was the custom for boys during the Spanish colonial times, he was then involved in the ecclesiastical music tradition of his town. In 1856, poverty led his parents to entrust him to the care of Augustinian priests in Intramuros, Manila who discovered his talent for music. In San Agustin Church, he apprenticed as a sacristan and a tiple. Under the friars, he was provided with daily sustenance, proper education, and access to musical environment but was also subjected to strict and harsh discipline.
Adonay has an absolute pitch, and supple, flexible voice which helped his musical learning despite having limited formal music education. His musicality delighted his choirmasters and he rose to the position of primer tiple. He mastered solfeggio, and learned chords, chord positions, and their resolutions on the organ by watching fellow organists. According to oral history, his proficiency in instruments includes the organ, piano, violin, contrabass, flute, and trumpet.