Nikephoros was born in 1002 to Michael Botaneiates and his wife, members of the Botaneiates family, a prominent military family from the Anatolic Theme. According to Attaleiates, Nikephoross grandfather Nikephoros and father Michael both served as commanders under Basil II () during his campaigns against the Georgians and his conquest of Bulgaria; Attaleiates is the only source which gives this information. Attaleiates also states that the Botaniati family was related to Byzantine Emperor Nicephorus II Phocas and the Phocas family. This was almost certainly used by Nikephoros to add legitimacy to his later rule, and this is corroborated by Psellos, who calls Nikephoros III "Phocas" in his reproduction of Byzantine Emperor Michael VII Doukas' letter to him. At an unknown date, Nikephoros married a woman named Vevdene, but he later married Maria of Alania, the former wife of Michael VII. He seems to have had at least one child with Vevdene, as Anna Komnene mentions his grandson in the "Alexiad". Little else is known of Nikephoross life before 1053, other than that he served as a commander under Emperor Constantine IX Monomachos during the Pecheneg revolt of 1048–1053.