Tommy Scott who was acting producer of Them sessions after Bert Berns returned to America described how "Mystic Eyes" came about in the studio as being originally conceived as an instrumental: "after blowing his harmonica for about seven minutes, Van suddenly burst into this spontaneous lyric." The ten-minute take was condensed to a single's length by cutting from the beginning and ending of the instrumental.
Tommy Scott, who temporarily oversaw production for Them sessions following Bert Berns' return to America, explained how "Mystic Eyes" came about in the studio: it initially started as an instrumental piece but evolved into a song when Van Morrison created lyrics on the spot after playing his harmonica for seven minutes. The resulting recording was later shortened.