Jughashvili set up a shop in the Russian Quarter of Gori, close to the barracks. In 1872 or 1874 he married Ekaterine (Keke) Geladze, a peasant girl who was probably 16. Keke, "an attractive freckled girl with auburn hair," was from the village of Gambareuli near Gori, and had moved to the town at a young age after her father died. They had three children, all boys, though the first two, Mikheil (born 14 February 1875) and Giorgi (born 24 December 1876), died aged two months and six months, respectively. Their third and final son, Ioseb, was born on 6 December 1878.

Suny writes that after the death of Mikheil, Jughashvili started to drink heavily, which only increased after the death of Giorgi, and that the marriage began to deteriorate. Kotkin has also suggested that rumours of infidelity by Keke took a toll on him, especially after the birth of Ioseb, with several men suggested as his possible father. However, Kotkin concedes that "whether Keke was flirtatious, let alone promiscuous, is unclear," and that "reliable evidence about the possible liaisons of the future Stalin's mother is lacking," and argues that Jughashvili was probably the father.

Jughashvili's shop was initially quite successful, employing up to ten people as well as apprentices, and the family initially enjoyed a rather high standard of living; a former apprentice would later note that he frequently saw butter in their home, which was an expensive delicacy for most Georgians (however Kotkin writes that the family lived more modestly, eating more traditional foods like lobio, lavash, and badrijani nigvzit). However, Jughashvili's drinking, exacerbated by a Georgian custom that business be paid in part with wine rather than money, had adverse effects on his business and home life. Isaac Deutscher felt that Jughashvili's inability to lift his status, "to be his own master," likely contributed to his drinking and frustrations. This idea is echoed by Robert Service, who noted that Jughashvili did not adapt to make European-style shoes that were popular at the time, and instead kept producing traditional Georgian styles, and suggests that the rumours about Keke were also a major influence on his drinking. Frequently drunk, Jughashvili became violent and routinely would beat Keke (who often hit back) and Iosef, and frequently fought in public, earning the nickname "Crazy Beso." Jughashvili's business suffered from his drinking, and he was eventually forced to give it up. The family also lost their home, and began staying with others for short periods, with nine different addresses over a ten-year period.

In 1884 Jughashvili left the family and moved to Tiflis. He returned to his old job at the Adelkhanov factory. He sent some money to Keke, as well as offers to reconcile, but all efforts to do so failed.

Jughashvili was upset when he learned that Keke had enrolled Ioseb in school, instead hoping his son would follow his path and become a cobbler. This led to a major incident in January 1890. Ioseb had been struck by a phaeton, severely injuring him. Jughashvili returned to Gori and brought his son to a Tiflis hospital, and after Ioseb healed he was apprenticed to the Adelkhanov factory. Keke was adamantly opposed to the idea and used her connections with the church to bring Ioseb back to Gori, where he would continue his studies to become a priest. This marked the last real contact Jughasvhili had with his wife or son, as he cut off contact and financial support when Ioseb left Tiflis.

Soon after Ioseb left Tiflis, Jughashvili seems to have left the Adelkhanov factory. He briefly made shoes in a stall at the Armenian bazaar in Tiflis, and his actions after that are uncertain. He did keep in contact with Ioseb, occasionally sending him hand-made shoes. Jughashvili also had one final role in Ioseb's life: in January 1900 Ioseb was arrested for the first time, on account of Jughashvili. When Jughashvili left Didi Lilo he was not removed from the village roles, and still owed taxes as a peasant from the region. It is not clear why Ioseb was arrested instead of his father, who still lived in Tiflis, but Kotkin suggests it was a police tactic to send a message to Ioseb, who had begun his revolutionary activities.

In August 1909 Jughashvili went to the Mikhailovsky Hospital in Tiflis, suffering from tuberculosis, colitis and chronic pneumonia. He died on 12 August 1909, with the cause of death listed as cirrhosis of the liver. Only one person, a fellow cobbler, attended his funeral, and he was buried in an unmarked grave in Telavi. The location of his grave was unknown until 1972, when Kandid Charkviani, the former First Secretary of the Georgian Communist Party, led efforts to find it and mark it, though it was not confirmed if Jughashvili's remains were still there. Charkviani had previously looked for photos of Jughashvili, at one point bringing several to Stalin to confirm their authenticity; after looking at them Stalin was unable to confirm if any were his father. There is only one photo purportedly of Jughasvhili, though its authenticity has never been confirmed.