He was born in Vienna, and became a favourite pupil of the Vienna court's Kapellmeister, Johann Joseph Fux. Wagenseil himself composed for the court from 1739 to his death. He also held positions as harpsichordist and organist. His pupils included Johann Baptist Schenk (who was to teach Ludwig van Beethoven), and Marie Antoinette. He travelled little, and died in Vienna having spent most of his life there.
Wagenseil was a well-known musical figure in his day--both Joseph Haydn and Wolfgang Amadeus Mozart are known to have been familiar with his works. His early works are Baroque, while later pieces are in the lighter galant style. He composed a number of operas, choral works, symphonies, concertos, chamber music and keyboard pieces.