Pecota attended Peterson High School in Sunnyvale, California. He was drafted by the Kansas City Royals in the tenth round of the 1981 January draft after playing at De Anza College in Cupertino, California. He batted .253 with 31 home runs and 267 runs batted in over six seasons in the Royals' farm system when he debuted with the Royals in September 1986.
Pecota accomplished the rare feat of getting his first major league RBI before his first major league hit. On September 22, in his sixth plate appearance, he drove in Jim Sundberg with a sacrifice fly. On September 25, he doubled off Frank Viola for his first major league hit.
He started the 1987 season with the Omaha Royals but was up in the majors by the end of April. He went back-to-back with Bo Jackson on May 8 for his first major league home run. Despite going 4-for-4 in the last game of his three-week stint in the majors to raise his season average to .556, Pecota was optioned back to triple A in mid-May. He was immediately recalled when third baseman George Brett went on the disabled list. He made a third trip to Omaha in late June, prompting the nickname "I-29" by his teammates, as Omaha is a short drive up Interstate 29 from Kansas City. Overall, he batted .276 with three home runs, fourteen RBIs and 22 runs scored backing up second, third and shortstop for the Royals. At the other end of I-29, he batted .310 with two home runs and sixteen RBIs.

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