By the time of the disbandment, there were only six Free Imperial Cities left: Augsburg, Bremen, Frankfurt, Hamburg, Lubeck, Nuremberg.

The rest were "Mediated", meaning absorbed into the surrounding respective territories, in the Mediation of 1806. This had to be done in response to Napoleon I's re-ordering of many cities and territories in the founding of the Confederation of the Rhine.

Within a few years, these remaining Free Cities were annexed either by German states such as Bavaria, or turned into puppet states by France, or directly annexed into France. Yet the Congress of Vienna restored the independence of several of them in 1815, although only with nominal independence. Finally, all of them were fully integrated into Nazi Germany.