The variations with coverage and annealing temperature in the adsorption structure of alanine on Ge(100) have been investigated using high-resolution core-level photoemission spectroscopy (HRCLPES). The C 1s, N 1s, and O 1s core-level spectra at a low initial coverage show that both the carboxyl and amine groups of the alanine molecules participate in bonding with the Ge(100) surface in an "intrarow O-H dissociated and N dative bonded structure". However, at higher coverage we found that in addition to this structure an "O-H dissociation structure" is present. Moreover, we systematically monitored the variation of the bonding features of alanine adsorbed on Ge(100) with annealing temperature and thus were able to track the desorption processes. By analyzing the C 1s, N 1s, and O 1s spectra at 420 K, we conclude that the principal adsorption structure at this temperature is the "O-H dissociation structure" because of the disconnection of Ge-N dative bonding. At higher temperatures, the "O-H dissociation structure" is converted into various fragments such as Ge oxide (or Ge-CO), Ge nitride (Ge cyanide), and Ge carbide.