Malchin's father was a member of the Mecklenburg legislature and he attended high school in Rostock, before being apprenticed to a surveyor in Schwaan, a town traditionally known as an artists’ colony.

He aspired to be a shipbuilder but was deemed not to have the requisite strength, so surveying won through. Two local artists inspired in him an interest in painting and from 1860 to 1862 he attended the Polytechnikum in Munich. Although he was ostensibly entered to study geodesy and engineering, in practice he spent more time in the local artists’ studios. He managed to complete his degree and qualified as an engineer, taking a position in the land surveying office of the Grand Duchy of Mecklenburg-Schwerin while continuing to paint in his spare time.

Malchin's paintings attracted the attention of the Ducal Court Painter Theodor Schloepke, who obtained a scholarship for him from Grand Duke Friedrich Franz II. Formal studies began in 1873 under Theodor Hagen at the Weimar Saxon-Grand Ducal Art School.

Despite the scholarship, he experienced continuing financial problems and his paintings did not prove commercially popular. Many were bought by the Grand Duke and his court for a nominal sum.

His circumstances improved considerably in 1879 when he was offered the position of art conservator and restorer for the Ducal collection. Obtaining a generous contract, he was free to pursue his own painting and he began to travel extensively.

In 1890, the new Grand Duke, Friedrich Franz III, promoted him to the rank of Professor. He retired in 1915 and was presented with the Knight's Cross of the Order of the Griffon by the Duke. A proposed retrospective of his work had to be cancelled due to the Greart War and was not presented until 1923, after his death. Approximately 260 of his paintings were in the possession of the Staatliches Museum in Schwerin. Ninety-two were destroyed during World War II. A street in Schwerin has been named after him.