Emidy spent the next four years aboard the Indefatigable during some of the biggest naval battles of the Napoleonic Wars, and was finally released from his duties in Falmouth in 1799. In Falmouth he began teaching and repairing instruments as well as giving concerts and performances. In 1802 Joseph Antonio Emidy married Jennifer Hutchins, the daughter of a local tradesman's daughter, at Falmouth Parish Church of King Charles the Martyr. Both their signatures were entered in the Marriage Register.
Over the next thirty years Emidy went on to form orchestral societies, give chamber and orchestral concerts across Cornwall and become the leading musical figure in the county. As well as performing works by celebrated composers of the day such as Gluck, Haydn, Cimarosa and Mozart, he composed many original orchestral and chamber works including violin and horn concertos. Tragically, none of his music has survived as it was never published but there are numerous accounts which testify to his extraordinary abilities and genius.