He was born in Bremen, and studied at the Kunstakademie Düsseldorf from 1890–95. His artistic studies during this period included visits to Belgium and Italy. Vogeler was a central member of the original artist colony in Worpswede, which he joined in 1894. In 1895 Vogeler bought a cottage there and planted many birch trees around it, which gave the house its new name: Barkenhoff. In 1901, he married Martha Schröder. He made book illustrations in an art nouveau style, and executed decorative paintings for the town hall of Bremen shortly before traveling to Ceylon in 1906. During a trip to Łódź, he studied Maxim Gorky's works, which resulted in the development of a deep sympathy for the working class. This feeling reached further heights when he saw life in the slums of Glasgow and Manchester during a trip. In 1908 he and his brother Franz founded the 'Worpsweder Werkstätte', which produced household objects. His paintings increasingly reflected his sympathy for the working class.
After the war he became a pacifist and joined the Communist Party of Germany. During the German Revolution of 1918–19, he joined the workers' and soldiers' council of the Bremen Soviet Republic, together with his friend Curt Stoermer. After the end of the Revolution, he was arrested for some time. It was at that time that he and his wife Martha were divorced. From that point on, he wanted to work ideologically, and the romanticism of his earlier work gave way to proletarian content. In 1931 Vogeler and his second wife Zofia "Sonja" Marchlewska, daughter of Julian Marchlewski, emigrated to Russia. After the German invasion of the Soviet Union he along with other German citizens was deported in 1941 to Kazakhstan by the Soviet authorities, and died there in 1942. KPD leader Wilhelm Pieck apparently had wanted to prevent his deportation, but Vogeler himself refused privileged treatment. As his wife Zofia and son Jan were Polish citizens they were drafted instead of being deported with him. Jan soon became a founding member of the National Committee for a Free Germany and after a long post-war academic career in Moscow died in his father's Worpswede in 2005. Zofia emigrated to Poland and died in Warsaw in 1983. Meanwhile, the Barkenhoff became a children's home. It was recently restored and has re-opened as a Heinrich Vogeler Museum in 2004. Late works from Heinrich Vogeler's ourvre appear to have some Egyptian influences, particularly in images such as Der Aufbau der zentralasiatischen Sowjetrepubliken. The influence remains in Worpswede amongst particular sculptures, and market performances.