Lignin is an aromatic plant compound that decomposes more slowly than other organic matter compounds; however, it was recently shown that lignin could decompose as fast as litter bulk carbon in minerals soils. In alpine Histosols, where organic matter dynamics is largely unaffected by mineral constituents, lignin may be an important part of soil organic matter (SOM). These soils are expected to experience alterations in temperature and/or physicochemical parameters as a result of global climate change. The effect of these changes on lignin dynamics remains to be examined and the importance of lignin as SOM compound in these soils evaluated. Here, we investigated the decomposition of individual lignin phenols of maize litter incubated for 2 years in-situ in Histosols on an Alpine elevation gradient (900, 1300, and 1900 m above sea level); to this end, we used the cupric oxide oxidation method and determined the phenols’ 13C signature. Maize lignin decomposed faster than bulk maize carbon in the first year (86 vs. 78% decomposed); however, after the second year, lignin and bulk C decomposition did not differ significantly. Lignin mass loss did not correlate with soil temperature after the first year, and even correlated negatively at the end of the second year. Lignin mass loss also correlated negatively with the remaining maize N at the end of the second year, and we interpreted this result as a possible negative influence of nitrogen on lignin degradation, although other factors (notably the depletion of easily degradable carbon sources) may also have played a role at this stage of decomposition. Microbial community composition did not correlate with lignin mass loss, but it did so with the lignin degradation indicators (Ac/Al)s and S/V after 2 years of decomposition. Progressing substrate decomposition toward the final stages thus appears to be linked with microbial community differentiation.