Shimerman co-authored a Star Trek: Deep Space Nine novel, The 34th Rule, with David R. George III, published January 1, 1999. It focuses on his character Quark who loses his bar and is imprisoned as a result of a diplomatic crisis between the Bajoran and Ferengi governments. The novel is an allegory for the internment of Japanese Americans during the Second World War
Shimerman has co-written a series of books in which he provides a science fictional basis for the life of Dr. John Dee. The first novel in the series, The Merchant Prince, was co-written with Irish author Michael Scott, known for his Nicholas Flamel series. Published in 2000, it features the historical figure John Dee being placed in suspended animation in 1575 by an alien race known as the Roc and awakening in 2099. The cover features Shimerman in Elizabethan garb. Shimerman commented: "John Dee really did exist. We're pretty sure he was a member of Queen Elizabeth's secret Service, which put it in his purview to kill if he needed to. The Elizabethan period was a much more perilous time; you had to be quick with a dagger and nefarious in order to survive". Shimerman thought there were aspects of both himself and his Star Trek: Deep Space Nine character, Quark, in the novel's interpretation of John Dee. Shimerman commented: "There are aspects of Quark similar to Dr. Dee, and undoubtedly there are aspects of Dr. Dee similar to Armin Shimerman, which would make him seem like Quark as well".
The other novels in the series are Outrageous Fortune (2002), co-written with Chelsea Quinn Yarbro, known for her historical horror novels, and Capital Offense (2003).
In 2008, he voiced the character of Wilmer in an audio dramatization of The Maltese Falcon that also featured Michael Madsen, Sandra Oh, and Edward Herrmann. In addition, he also voiced the character of Mr. Phillips in Focus on the Family Radio Theatre's production of Anne of Green Gables. He also voiced Raanu in the straight-to-DVD animated film Bionicle: The Legend Reborn. He also voices Green Goblin in the video game Marvel: Ultimate Alliance 2.
In 2011, he provided additional voices for the MMORPG Star Wars: The Old Republic.
In 2012, he also provided additional voice talent for the MMORPG The Secret World.