Biolog EcoPlates™ can be used to measure the carbon substrate utilisation patterns of microbial communities. This method results in a community-level physiological profile (CLPP), which yields a very large amount of data that may be difficult to interpret. In this work, we explore a combination of statistical techniques (particularly the use of generalised additive models [GAMs]) to improve the exploitation of CLPP data. The strength of GAMs lies in their ability to address highly non-linear relationships between the response and the set of explanatory variables. We studied the impact of earthworms (Aporrectodea caliginosa Savigny 1826) and cadmium (Cd) on the CLPP of soil bacteria. The results indicated that both Cd and earthworms modified the CLPP. GAMs were used to assess time-course changes in the diversity of substrate utilisation (DSU) using the Shannon-Wiener index. GAMs revealed significant differences for all treatments (compared to control -S-). The Cd exposed microbial community presented very high metabolic capacities on a few substrata, resulting in an initial acute decrease of DSU (i.e. intense utilization of a few carbon substrata). After 54 h, and over the next 43 h the increase of the DSU suggest that other taxa, less dominant, reached high numbers in the wells containing sources that are less suitable for the Cd-tolerant taxa. Earthworms were a much more determining factor in explaining time course changes in DSU than Cd. Accordingly, Ew and EwCd soils presented similar trends, regardless the presence of Cd. Moreover, both treatments presented similar number of bacteria and higher than Cd-treated soils. This experimental approach, based on the use of DSU and GAMs allowed for a global and statistically relevant interpretation of the changes in carbon source utilisation, highlighting the key role of earthworms on the protection of microbial communities against the Cd.