The thermal stability of different organic layers on silicon has been investigated by in situ infrared spectroscopy, using a specially designed variable-temperature cell. The monolayers were covalently grafted onto atomically flat (111) hydrogenated silicon surfaces through the (photochemical or catalytic) hydrosilylation of 1-decene, heptadecafluoro-1-decene or undecylenic acid. In contrast to alkyl monolayers, which desorb as alkene chains around 300 degrees C by the breaking of the Si-C bond through a beta-hydride elimination mechanism, the alkyl layers functionalized with a carboxylic acid terminal group undergo successive chemical transformations. At 200-250 degrees C, the carboxyl end groups couple forming anhydrides, which subsequently decompose at 250-300 degrees C by loss of the functional group. In the case of fluorinated alkyl chains, the C-C bond located between CH2 and CF2 units is first broken at 250-300 degrees C. In either case, the remaining alkyl layer is stable up to 350 degrees C, which is accounted for by a kinetic model involving chain pairing on the surface.