The first death camp to be constructed under Thomalla's supervision was Bełżec. Construction started on 1 November 1941 and was completed in March 1942. He then proceeded to design and supervise the construction of Sobibor in March 1942. Workers employed for building the camp were local people from neighboring villages and towns. During this preliminary stage, Thomalla served as the head of the Sonderkommando at Sobibor. The Sonderkommando consisted of about eighty Jews from ghettos within the vicinity of the camp, brought to Sobibor for construction work. A squad of ten Ukrainians trained at Trawniki concentration camp guarded the Sonderkommando. Upon completion of the camp, these Jews were shot. When Thomalla completed his building assignment in Sobibor he was replaced there by Franz Stangl in April 1942. He then proceeded to Treblinka which copied the design of Sobibor.
SS-Unterscharführer (Corporal) Erwin Lambert who had previously been assigned to the Action T4 euthanasia program and had constructed the new gas chambers in Treblinka, testified about Thomalla:
I and Hengs went to Treblinka by car. SS-Hauptsturmführer Richard Thomalla was the camp commander. The Treblinka camp was still in the process of construction. Thomalla was in Treblinka for about four to eight weeks. I was attached to a building team there. Thomalla was there for a limited time only and conducted the construction work of the extermination camp. During that time no extermination actions were carried out. Then Dr. Eberl arrived as camp commander. Under his direction the extermination Aktionen of the Jews began.
Between July 1942 and October 1943, around 850,000 people were killed in Treblinka. Thomalla was reportedly executed by the NKVD (Soviet Police) in Jičín, Czechoslovakia on 12 May 1945.