Soil microorganisms are one of the main components of the soil ecosystem and play an important role in agro-ecosystem function and sustainable agricultural development. Arbuscular mycorrhizal fungi (AMF) are important components of soil microbial communities because of their symbiotic relationships with many crop species. The increase in potato production area in the south mountain region of Ningxia, China, made crop rotation difficult and long-term potato monoculture led to significant yield reductions due to pests and devastating diseases. Plant complementarity may decrease interspecific competition through resource partitioning, and facilitation may improve the availability of resources. AMF seem to play an important role in these interactions, so intercropping potatoes with a different crop species and AMF may moderate yield reductions in a long-term potato monoculture system. The objective of this study was to investigate soil microbial community composition and the changes in AMF diversity due to the transition from continuous potato monoculture to an intercropping system. We studied two different intercropping systems, maize-potato and faba bean-potato, in a field where a potato monoculture system had been applied continuously for 10 a. The composition and the functional diversity of soil microbial communities were accessed by measuring the phospholipid fatty acids contents (PLFA) and by community level physiological profiles (CLPPs) using the Eco-plate technique. Then we identified AMF by morphological characteristics and calculated their relative abundance. The results showed that soil microbial community structures changed with the transition from continuous potato monoculture to the intercropping system. In the maize-potato intercropping system, PLFA levels decreased, whereas the metabolic activity of microbial functional groups, as well as the carbon utilization of carboxylic acid, polymer compounds, aromatic compounds, and amino acids, increased. In the faba bean-potato intercropping system, only carbohydrate utilization by microorganisms increased. The total PLFA content was lower in the maize-potato intercropping system than in the faba bean-potato system. The biomasses of gram-negative bacteria, gram-positive bacteria, Pseudomonas, and AMF were lower by 35.1%, 28.0%, 24.8%, and 9.0%, respectively, in the maize-potato intercropping system than in the continuous monoculture system. Conversely, the fungal biomass was higher by 21.1% in the maize-potato intercropping system than in the continuous monoculture system. However, there was a reverse tendency in the faba bean-potato intercropping system. AMF species richness decreased in the continuous monoculture system compared to the faba bean-potato intercropping system, while the dominant species in the latter was Ganoderma formosanum. The change in AMF dominant species might be restricted by some integrated factors, including the symbiotic relationship with different crops and the diversity of soil microorganism structure and function. These results suggest that the performance of soil microbial communities is not always consistent with changes in the structure of soil microbial functional groups in intercropping systems. The maize-potato intercropping system may enhance the diversity of soil microbial functional groups, whereas in the faba bean-potato intercropping system, the diversity of soil microbial functional groups is higher. We may conclude that different microbial species have different rhizosphere effects on potato cultivation.