The characterization of fungal diversity through metabarcoding requires standardized workflows to avoid methodological biases and generate reliable, reproducible data. In this context, this research initially proposes an introductory good practice guide for fungal metabarcoding in general, addressing critical steps ranging from sampling design and DNA extraction to barcode selection and statistical analyses. Complementarily, the study narrows its focus to Arbuscular Mycorrhizal Fungi (AMF), detailing the methodological particularities of this group and introducing ALMA, an automated bioinformatics pipeline exclusively developed to maximize the accuracy of Glomeromycota taxonomic classification via phylogenetic placement. In an applied manner, the pipeline was utilized and validated in the second chapter, which investigated the impacts of converting the Amazon forest into agricultural areas on AMF communities and glomalin-related soil protein (GRSP) dynamics in the Arc of Deforestation (Mato Grosso, Brazil). Combining morphological analyses and metabarcoding (eDNA), the study recorded a complete taxonomic reorganization (species turnover) rather than a loss of biodiversity. In total, 128 taxa were identified: the morphological approach detected 75 morphospecies (39 in the forest and 58 in the cropland), while metabarcoding identified 61 OTUs (41 in the forest and 41 in the cropland). Agricultural management homogenized the environment, increasing soil pH and nutrients, which triggered a functional transition of guilds: ruderal strategies (Glomerales) dominant in the forest gave way to stress-tolerant (Acaulosporaceae) and competitive (Gigasporales) taxa in the cropland. Furthermore, the agricultural area exhibited intense disturbance-induced sporulation and a functional coupling between the AMF community and glomalin accumulation, supporting in the stabilization of soil organic carbon. Demonstrating that, although intensive agriculture disrupts the original forest ecological networks, this impact selects AMF lineages more tolerant to continuous stress, evidencing the soil's capacity for biological reorganization as a resilience mechanism against degradation. Finally, this study significantly contributed with new species records for the Legal Amazon, increasing the known richness to 161 species, 135 within the Brazilian Amazon context, and added 20 new records to the national funga.