As a composer Schaffrath limited himself to instrumental music including symphonies, keyboard pieces, sonatas and concertos. The harpsichord sonatas were almost all fast-slow-fast settings and the opening movements were most often scored in ABA form. Many of the keyboard compositions were simple two-part formulations with the left hand playing the lesser role. Schaffrath's music can be considered transitional, including pieces which are stylistically galant (between the Baroque and the Classical), characteristically melodious and composed of short phrases using triplets and steady rhythms. He composed counterpoint as found in his orchestral music, but most of his music lacked an expressive fervor. The majority of his works may now be found in the state library in Berlin, where he died.
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.