Sisko had been married to Sarah Sisko; unknown to him at the time, however, Sarah's body had been occupied by a Prophet to see that their Emissary was born. When the Prophet left Sarah a year after Benjamin was born, Sarah left as well. After her disappearance and ultimate death, Joseph Sisko remarried and had at least three other children with his new wife: Judith and at least two other boys. (DS9: "Homefront", "Paradise") Joseph was a master chef and owner of the restaurant Sisko's in New Orleans on Earth. He passed on his excellent cooking skills to Benjamin and Jake.
After the Dominion bombing at Antwerp, his son, grandson and Odo traveled to Earth. Shortly after, Starfleet authorities on Earth, with assistance from Benjamin Sisko and Odo, made it mandatory for the families of all Starfleet officers to undergo blood screenings. He resisted this, and complained that his freedoms were being usurped by the government. (DS9: "Homefront", "Paradise Lost")
Later that year, in spite of the Dominion War, he left Earth for the first time to visit his son and grandson on Deep Space 9. During his visit, Benjamin was sent a vision by the Prophets in which Joseph took the role of a 1950s preacher. (DS9: "Far Beyond the Stars")
When Ben left his post on Deep Space 9 following the murder of Jadzia Dax and the disappearance of the Bajoran wormhole, he moved into his father's home. It was here that Ben had visions of a Sarah Sisko. Although refusing to do so at first, Joseph would explain that Sarah was Ben's real mother who left after his birth. Joseph then accompanied his son to Tyree in search of answers as to who Sarah really was and to find the Orb of the Emissary that would release the prophets and re-activate the Wormhole. (DS9: "Image in the Sand", "Shadows and Symbols")
Joseph dies of complications caused by pre-existing health problems in 2381, in the novel Rough Beasts of Empire.