Born in Alicante, he also attended the Conservatorio Superior de Música Oscar Esplá there, where he studied the theory of harmony as well as bassoon. He moved to the Netherlands in 1996 to study the historical bassoon there. He studied bassoon and chamber music under Donna Agrell at the Königlichen Konservatorium in Den Haag, as well as music theory under Peter van Heyguen. Javier Zafra gained his diploma in Baroque bassoon with distinction in June 2000.
He was a member of the European Union Baroque Orchestra (EUBO) in 1997, then under the baton of Ton Koopman. He has since played with the ensembles Anima Aeterna, Orchestre des Champs Elysées, Concert d’Astrée, and Al Ayre Espanol. His prime interest is in chamber music. He is a member of the Nachtmusik wind sextet (Eric Hoeprich) and founded the els Sonadors de Martin i Soler wind octet. He was also the founder of the orchestra Le Cercle de l’Harmonie in Paris, where he lives. Javier Zafra has been an established member of the Freiburg Baroque Orchestra since 1999