Having been given some lessons by Schumann in his youth, Merkel spent most of his career in Dresden, concentrating on organ-playing from 1858. A Lutheran himself, he nevertheless held an appointment at one of Dresden's main Catholic churches from 1864 until his death. During the same period he taught the organ at Dresden's Conservatorium.
His compositions include nine organ sonatas (which have been recorded several times, as well as occurring quite often in organ recitals), plus a separate sonata for two organists (his Opus 30), and several dozen miniatures (some of them based on Protestant chorale melodies). In these works his style is broadly conservative, very much influenced by Mendelssohn, and with similarities to the output of his younger contemporary Josef Rheinberger. He also produced choral and piano pieces.