Heavy metals far in excess of trace amounts that are required for healthy plant growth, cause harmful effects on soil microorganisms; however, studies concerning the characterization of microbial communities in mine soils are scarce. The present study is the first attempt to characterize, by means of the analysis of phospholipid fatty acid (PLFA) patterns, soil microbial community composition from a contaminated mine soil (Pb, As) subjected to different remediation technologies. A pot experiment was performed with a soil from the São Domingos mine (South of Portugal) with or without native herbaceous plants combined with the following soil treatments: control; inorganic fertilizer (NPK); inorganic fertilizer plus polyacrylate polymer; inorganic fertilizer plus organic amendment (compost); inorganic fertilizer plus both amendments (compost, polymer). The measurements of PLFA patterns were made on soil samples collected 5 months after the application of remediation treatments. The total microbial biomass and the biomass of specific groups increased notably after soil treatments, particularly those including organic amendments, and were significantly higher in presence of native plants than in the corresponding bare soils. The data also indicated that a plant cover rather than organic and inorganic treatments played the dominant role in determining the composition of the microbial community. An influence of different soil treatments on microbial composition was also observed; the effect of organic amendment being more pronounced than that of the remaining treatments. The results clearly showed the efficacy of a vegetation cover (native plants) combined with the use of organic amendment in the reclamation of this degraded mine soil.