In 1831 Weber was appointed to the chair of physics at Göttingen and there followed 6 years of close friendship and collaboration with Gauss. Weber developed sensitive magnetometers and other magnetic instruments during this time.

When Victoria became Queen of Britain in 1837 her uncle became ruler of Hanover and revoked the liberal constitution. Weber was one of 7 professors at Göttingen to sign a protest and all were dismissed. He remained at Göttingen without a position until 1843 when he became professor of physics at Leipzig.

In 1848 he returned to his old position in Göttingen and, in 1855, he and Dirichlet became temporary directors of the astronomical observatory there. His work on the ratio between the electrodynamic and electrostatic units of charge in 1855 proved extremely important and was crucial to Maxwell in his electromagnetic theory of light. Weber found the ratio was 3.1074 10⁸ m/sec but failed to take any notice of the fact that this was close to the speed of light.

Weber's later years at Göttingen were devoted to work in electrodynamics and the electrical structure of matter. He was described by Thomas Hirst in the following way:

He speaks and stutters on unceasingly, one has nothing to do but listen. Sometimes he laughs for no earthly reason, and one feels sorry at being not able to join him.