A revolution in sequencing and bioinformatics technology has led to a steep increase in research studies that include microbial community characterization. Many of these studies utilize amplicon sequencing, targeting bacteria and fungi and seek to draw correlations between the presence and abundance of certain taxa and soil properties indicative of soil health. More recently, shotgun metagenomics have been applied to soils to investigate the microbial community’s functional potential. This chapter will describe the methods used in generating amplicon and metagenomics data, emphasizing key decisions that researchers must make in the workflow that can influence community composition descriptions. We will discuss the pros and cons of these approaches and the scope of inference that sequencing data has in connection to the healthy functioning of soil.