Johannes Søbøtker was born on St. Croix in the Danish West Indies, the son of planter and later General War Commissioner Adam Levin Søbøtker (1753–1823) and Susanne van Beverhoudt (1761–1811).

His father owned the estates Constitution Hill and Høgensborg on Saint Croix and was for a while the largest landowner on the islands.

Søbøtker was sent to Copenhagen where he received a commercial education first in De Coninck & Co. and later his future father-in-law Lars Larsen's trading house.

When his father died in 1823 on St. Croix, he inherited the plantations, Constitution Hill and Høgensborg.

He introduced the first steam mill in the Danish West Indies on his plantation Høgensborg.