On a global scale, the production of foods of plant origin has caused the overexploitation of the soil and the alterations of agroecosystems due to the indiscriminate use of agrochemicals and climate change. For this reason, it is necessary to establish good agricultural practices in soil management and the cultivation of different plant species of food interest. The study of the multiple biogeochemical processes that occur in arable soils, the physiological, biochemical, and molecular responses that occur in plants and the microbial activity that is associated with plant roots reveal key information about the functionality of each biological element that co-interacts with the soil. The establishment of protocols for the collection of soil samples, rhizospheric microorganisms, and plant tissues such as roots allow the processing of samples in an easy way for the subsequent obtaining of reliable results by executing a particular analysis method. This chapter describes in detail three efficient protocols for sampling and storage of agricultural soil, rhizosphere, and root tissue. The correct handling of these samples allows the extraction of chemical elements and metabolites in plant tissues and the physicochemical analysis in the soil and the isolation of filamentous fungi, yeasts, bacteria, and nematodes from the rhizosphere.