Following his PhD, Fichtner spent two years as a young researcher at the former Karlsruhe Nuclear Research Center (KfK) and developed his method further so that it could be applied to organic materials also. In 1994 he became assistant to the board of directors of the Karlsruhe Research Center (FZK), in the area Basic Research and New Technologies, with Herbert Gleiter as director. In 1997 he left to build up a new activity on microprocess engineering, with a focus on heterogeneous catalysis in microchannels, for fuel processing (methanol steam reforming, partial oxidation of methane) and synthesis of chemicals. The group was eventually integrated in the new Institute for Microprocess Engineering in 2001. In 2000 he was offered a position at the new Institute of Nanotechnology, INT (Founding directors: Herbert Gleiter, Jean-Marie-Lehn, Dieter Fenske) to build up a new activity on nanoscale materials for energy storage. Since then he is group leader there. In 2012 he received a call by the Ulm University to become a professor (W3) in Solid State Chemistry, which he accepted in 2013. The position is connected to a function as group leader at the new Helmholtz Institute Ulm. Since 2015 he has been executive director of the institute.
Fichtner has co-ordinated several EU projects and collaborative projects from the German ministries of Economy and Research and Education. He has been organizer of various symposia at MRS and GRC conferences, and he was Chair of the GORDON Research Conference on Metal-Hydrogen Systems in 2013 and of the 1st International Symposium on Magnesium Batteries (MagBatt) in 2016.