A series of ligands, which terminate with ditopic bipyridines connected by a variable central bridge, fluorene biEDOT or azo-benzene, have been investigated by high-resolution scanning tunneling microscopy (STM). The bipyridines can form different hydrogen bonds or can coordinate with transition metal ions at the solid/liquid interface. Their interactions allow such molecules to self-assemble on HOPG. The bridges provide redox-active, photoactive, or fluorescent functionalities. Both the bipyridine terminals and the bridges are units able to switch the molecules in terms of structure organization and electronic properties. Multi-functional switches or transitions are thus generated, for example (i) protonation generates a molecular cis-like to trans-like isomerization and switches the nanoscale organization of the molecule on the surface, (ii) Co(II) cations react with the pyridines to generate on-surface coordination complexes, and (iii) changing the central bridge induces different self-organized structures on the surface. A series of bpy-X-bpy molecules showing different molecular isomers, structural phase transitions and coordination configurations have thus been revealed by means of high-resolution STM.