In December 2005, Peach Pit announced that they were working on a new shōjo manga series called Shugo Chara! The first chapter was published in the February 2006 edition of Nakayoshi magazine. The first volume collection was then republished on July 6, 2006 by Nakayoshi publisher Kodansha. In addition to the regular volumes, the series is being released in limited editions in Japan, each of which include different cover art from the regular editions, metallic foil sleeves, and a set of postcards featuring Amu in various outfits and poses following the color theme of the dust jackets.Del Rey Manga announced that it acquired the English language rights to Shugo Chara! during MangaNEXT 2006 and released the first volume on March 27, 2007. Kodansha Comics USA will keep publishing the series in 2011.

The series was put on hiatus along with two other series, Rozen Maiden and Zombie-Loan, in December 2008 due to a sudden illness and hospitalization. One month later, Peach-Pit announced that all three series will resume and thanked their fans for the support during the illness.

There is a spin off manga series called Shugo Chara Chan!, featuring drawings by Mizushima Naftaren, which is in yonkoma (4-panel) comics style and focuses on Amu's guardians. Currently there are three volumes. There is no special edition version of the spin off series.

The January issue of Kodansha's Nakayoshi magazine confirmed on December 1, 2009 that Peach-Pit would be ending the Shugo Chara! manga in the next issue on December 28. A sequel series was later announced, titled Shugo Chara! Encore!, and began in the April 2010 issue of Nakayoshi.