Bayerschmidt began his career with Bayern Munich, and made his debut for the club in October 1986, as a substitute for Holger Willmer in a European Cup match against PSV Eindhoven. Bayern reached the competition's final that season, and Bayerschmidt was an unused substitute as they lost against FC Porto. They also won the Bundesliga title, with Bayerschmidt making one appearance, replacing Michael Rummenigge in a 3–2 win over Werder Bremen. He made a further three appearances the following year, and the last match of the season brought his first goal – he scored Bayern's second as they turned around a 3–0 deficit against Bayer Leverkusen to win 4–3. However, Werder Bremen had already wrapped up the title, so Bayern finished in second place.