Thousands of fans took the chance to witness the Catalan's first training session as Bayern coach, which was held in the Allianz Arena, and Kroos was one of 16 first-team regulars on the field.
Others present included Philipp Lahm, Manuel Neuer, Franck Ribery, Thomas Muller and Jerome Boateng - players who lifted the Champions League trophy at Wembley just a month ago.
Kroos missed that game due to an abductor injury suffered in a quarter-final meeting with Juventus but, after a two-and-a-half-month break, he was back in training on Wednesday.
All eyes were on Guardiola's debut as Bayern coach two days after his official presentation on Monday.
After a warm-up, he began to reveal some of his preferred training drills. Some of those employed suggested his successful possession-based brand of football from Barcelona will also be used at Bayern.
"It was interesting, the impressions were positive," attacking midfielder Thomas Muller told Sport1 television.
"It was a good first meeting. He spoke well to us and we had a good session, so I'm very happy."
New signing Mario Gotze was unable to train due to the muscular injury which ruled him out of the end of the season for his former club Borussia Dortmund while Holger Badstuber remains sidelined with torn cruciate knee ligaments.
Bastian Schweinsteiger is expected to start training in the coming days while the contingent of players involved at the Confederations Cup will link up with the squad after a holiday.
Bayern will train again at the Allianz Arena on Thursday before returning to their usual Sabener Strasse training facilities.
And from July 4, they will move to a week-long training camp in northern Italy.