In 1874, Cleve married Carolina Alma "Caralma" Öhbom (known as Alma Cleve), a teacher and author; the couple had three daughters. The first daughter, Astrid Maria Cleve (born 22 January 1875), became a botanist. His son-in-law and grandson, Hans von Euler-Chelpin and Ulf von Euler, both won Nobel Prizes. Cleve was friends with Thomas Edward Thorpe. The second daughter, Agnes Cleve-Jonand (born Agnes Elisabet Cleve) (1876-1951), was a visual artist and pioneer of Modernism in Sweden. The third and last daughter, Célie Brunius (born Gerda Cecilia Afrodite Cleve) (1882-1980), was a journalist. His daughter Agnes was married to illustrator, set designer and artist John Jon-And. His daughter Célie was married to writer August Brunius and was the mother of artist Göran Brunius, journalist Clas Brunius and associate professor Teddy Brunius. The television host and politician Lisette Schulman was his great-granddaughter.
Per Teodore Cleve was a supporter of women's equality and Ellen Fries, the first Swedish woman to receive a PhD, was one of his students.
Cleve began experiencing pleurisy in December 1904 and it affected his heart. He thought that he had recovered by the spring of 1905, and he returned home to Uppsala, Sweden,. but he died there on 18 June 1905.