Bayes started his career at Brentford, where he progressed through the youth system to make his first-team debut in March 1990. He made just a handful of appearances during his time at Griffin Park, and in 1993, joined Torquay United on a free transfer. Bayes played regularly during his time at Torquay, making over 100 appearances during his three seasons in Devon. He then joined Exeter City in July 1996, and spent three years with the club playing regularly. Bayes returned to London in July 1999 when he signed for Leyton Orient. After three years at Orient, Bayes joined League of Ireland team Bohemians in 2002, winning the league title in his first season with the club.