In this perspective, we aim to describe the unique challenges of studying microbial communities in soil ecosystems, and to address common misconceptions in the analysis and interpretation of amplicon sequencing data. Patterns often arise in community data, but the interpretation of these patterns in a soil context remains challenging and limited due to the poor link between the sequenced marker gene regions and microbial functions, as well as the compositional nature of the data itself \citep{Blanchet_2020}. We provide suggestions for designing sequencing experiments and analyzing data to gain improved insights into microbial community structure and dynamics within the context of the complex soil environment. Amplicon sequencing, when used as part of a well-designed experiment, represents an informative approach for investigating microbial community structure and correlations between taxa and environmental parameters, as well as for developing new hypotheses regarding microbial community dynamics.