Schaffrath was born in Hohnstein. He applied to be organist at the Sophienkirche in Dresden, but did not receive this position (Wilhelm Friedemann Bach was favoured for it). He did serve in the court of the Crown Prince Frederick (Frederick the Great) as a harpsichordist in the orchestra. From 1741, however, he was strictly the musician to the King's sister, Amalia.
As a composer Schaffrath limited himself to instrumental music including symphonies, keyboard pieces, sonatas and concertos. Schaffrath's music can be considered transitional, including pieces which are stylistically galant (between the Baroque and the Classical). The majority of his works may now be found in the state library in Berlin.
He composed many types of music. He was most notable for overtures, symphonies, harpsichord concerti, quartets, trios, duets for a solo instrument and obbligato harpsichord, and sonatas for harpsichord.