Jonathan Peirce was born on October 18, 1809, in Boston, Massachusetts, to Jonathan and Lydia Peirce. His father was a blacksmith and a Revolutionary War veteran. The family moved to Charlestown, Massachusetts, around 1811, and he grew up there. At the age of fifteen, he began working as an apprentice pump and block maker. He sailed aboard the Clio in May 1827, and he spent the next two years visiting Brazil, Chile, and California.
He married Elizabeth Leavitt on October 26, 1835, and they had at least five children: Jonathan, born on August 26, 1836; Abby, born on September 27, 1838; William, born on April 28, 1841; Joshua, born in 1848; and Elizabeth, born on October 22, 1849. In 1841, he established his own pump and block making business in Boston.
He supported the Know Nothing Party, and newspaper editors floated him as a gubernatorial candidate in 1854. He served in the state legislature in 1855. In the election of 1856, however, he privately supported Republican presidential candidate John C. Frémont. He argued that, if Frémont “is elected no aliens or Roman Catholics will be retained in office.”
In the fall of 1861, he received a commission as a captain in the 1st Massachusetts Infantry Battalion, which later became the 32nd Massachusetts Infantry. He resigned on May 22, 1862. His commanding officer reportedly claimed that he was too "old to be a soldier." In response, Peirce argued that the "country may yet want the services of old men who are true to her interests in preference to young men who lack principle." He died in Chelsea, Massachusetts, on August 6, 1867.