He married Sarah "Lois" Shepard in November 1919, she being six years older than he was and having a son from a previous marriage. Together they had nine children. In 1928, Neibaur had an accident at the sugar beet factory where his arm was severely mangled in a cutting machine. Workers had to disassemble the machine to free his arm. The Neibaurs had three sons who died from accidents: one (18 months old) drowned in an abandoned cesspool; another (two years) was killed by an automobile; and one (six years) died from burns and infection from a wood-burning stove.