Malcolm’s first wife was Ingibiorg, daughter of Finn Arnesson, Jarl of Holland, and by her he had nine children including Duncan II King of Scots, born in 1060 and murdered in 1094. Duncan had married in 1090 Ethelreda, daughter of Gospatrick Earl of Northumberland.

The Orkneyinga saga reports that Malcolm married the widow of Thorfinn Sigurdsson, Ingibiorg, a daughter of Finn Arnesson.[34] Although Ingibiorg is generally assumed to have died shortly before 1070, it is possible that she died much earlier, around 1058.[35] The Orkneyinga Saga records that Malcolm and Ingibiorg had a son, Duncan II (Donnchad mac Maíl Coluim), who was later king.[5] Some Medieval commentators, following William of Malmesbury, claimed that Duncan was illegitimate, but this claim is propaganda reflecting the need of Malcolm's descendants by Margaret to undermine the claims of Duncan's descendants, the Meic Uilleim.[36] Malcolm's son Domnall, whose death is reported in 1085, is not mentioned by the author of the Orkneyinga Saga. He is assumed to have been born to Ingibiorg.[37]
Malcolm's marriage to Ingibiorg secured him peace in the north and west. The Heimskringla tells that her father Finn had been an adviser to Harald Hardraade and, after falling out with Harald, was then made an Earl by Sweyn Estridsson, King of Denmark, which may have been another recommendation for the match.[38] Malcolm enjoyed a peaceful relationship with the Earldom of Orkney, ruled jointly by his stepsons, Paul and Erlend Thorfinnsson. The Orkneyinga Saga reports strife with Norway but this is probably misplaced as it associates this with Magnus Barefoot, who became king of Norway only in 1093, the year of Malcolm's death.[39]