Rudbeck's research led to the Queen's support of his career. To facilitate his studies of human anatomy, he had a cupola built on top of Gustavianum, a university edifice, and in it was built an arena-like Theatrum anatomicum, where dissection could be carried out in front of students. The cupola still remains and is a landmark in Uppsala. The "Gustavianum" stands in front of the cathedral, and is still part of the university.
Between 1679-1702, Rudbeck dedicated himself to contributions in historical-linguistics patriotism, writing a 3,000-page treatise in four volumes called Atlantica (Atland eller Manheim in Swedish) where he purported to prove that Sweden was Atlantis, the cradle of civilization, and Swedish the original language of Adam from which Latin and Hebrew had evolved. His work was criticized by several Scandinavian authors, including the Danish professor Ludvig Holberg, and the Swedish author and physician Andreas Kempe, both of whom wrote satires based on Rudbeck's writings. His work was later used by Dennis Diderot in the article "Etymologie" in Encyclopédie as a cautionary example of deceptive linking of etymology with mythical history.
Despite the criticism targeting his linguistic theories and despite the priority dispute with Bartholin, Rudbeck remained a national icon in Sweden for many years. His son, Olof Rudbeck the Younger, continued his linguistic work and also became involved in providing an "intellectual reason" for power during a period when Sweden aspired to a position as one of the great powers of Europe. Rudbeck the Younger added speculations about the relationship between Sami and Hebrew languages to his father's long list of fantastical linguistic relationships.
During the course of a fire that destroyed most of Uppsala in 1702, a large portion of Rudbeck's writings was lost. Rudbeck himself directed the people of the city, shouting orders from a roof while his house burned down. He died the same year, shortly after the fire, and was buried in Uppsala Cathedral at the transept. (Since then, Swedish monarchs have frequently been crowned over his grave.)
Alfred Nobel, the founder of the Nobel Prizes, was a descendant of Rudbeck through his daughter Wendela, who married one of her father's former students, Peter Olai Nobelius.
The plant genus Rudbeckia was named by the botanist Carolus Linneaus in honor of both Rudbeck and his son.