Knoedler was originally drafted by the St. Louis Cardinals in the 41st round (1218th overall) in the 1998 Major League Baseball Draft out of Springfield High School but did not sign with them. He was also taken in the 13th round (391st overall) of the 2000 MLB Draft (after playing at Lincoln Land Community College) by the San Francisco Giants. Once again, he did not sign and chose to play college ball at Miami University. He entered the draft again in 2001, being taken by the Giants again, this time as a higher overall pick (166th overall in the 5th round). This time he signed a contract.\n', '

Knoedler began his professional career in 2001 as a pitcher for the Low-A Salem-Keizer Volcanoes. He appeared in 13 games, all in relief, and had a 1-1 record with a 1.26 ERA. He did long relief, pitching 28​2⁄3 innings with 38 strikeouts and only walked 9.\n', '

In 2002, Knoedler converted to catcher. He played for the Single-A Hagerstown Suns and in his first year as a catcher, he batted .257 with 5 home runs in 86 games. Knoedler was promoted to the High-A San Jose Giants in 2003. His batting average was the same from the previous year, but he doubled his home run total to 10.\n', '

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