Jonathan Velasco sang with the University of the Philippines Madrigal Singers under Prof. Andrea Veneracion in 1981 to 1989, becoming its assistant choirmaster a year after he joined. In 1989, he started his studies in Choral Conducting at the Berliner Kirchenmusikschule under Martin Behrmann and finished with distinction. He was a member and assistant conductor of the World Youth Choir, and for the 1996 summer session became its first Asian conductor.
He has been a member of the jury in choral competitions in Europe and Asia. In 1993 he joined the faculty of the Asian Institute for Liturgy and Music in Manila, where he held the post of Chairman of Choral Studies until 2008. He is currently a lecturer for Voice at the University of the Philippines College of Music.
Velasco regularly holds choral clinics and workshops in Manila as well as in Germany, France, Sweden, Spain, the Netherlands, the United States, Israel, Japan, China, Indonesia, Taiwan, Thailand, Malaysia and Singapore. Together with his choirs, he has won first prizes in choral competitions in Maribor (Slovenia), Cork (Ireland), Marktoberdorf (Germany), and Tolosa (Spain). He currently conducts the Ateneo Chamber Singers.
Velasco is a member of the artistic committee of the Polyfollia Festival in St. Lo, France. He was also a member of the artistic committee of the 8th World Symposium on Choral Music held in Copenhagen, Denmark, in July 2008. He is an adviser to the board of the International Federation for Choral Music, and is the Philippine representative to the World Choir Council. In January of 2008, he was elected the first President of the newly formed Philippine Choral Directors