Advances in genomic laboratory and bioinformatics techniques have allowed us to infer microbial ecology information from genomes. This ability has led to great advances in microbiome science; however, there is not yet a standard comprehensive workflow for functional annotation. Some software tools annotate metabolic functions, but the new tool 'METABOLIC' improves upon this and expands into biogeochemical pathways like the carbon cycle. METABOLIC takes sequence inputs from isolates, metagenome-assembled genomes, or single-cell genomes. The data can be processed through two workflow scales: genome and/or community. The genome-scale workflow annotates the genomes and validates motifs of conserved protein residues. It also analyzes metabolic pathways and calculates the microbial contributions to individual biogeochemical processes and cycles. The community-scale workflow adds to this by first determining the genome abundance in the microbiome. It can then determine potential metabolic handoffs or exchanges and estimate microbial contributions to biogeochemical cycles. METABOLIC also offers visualization tools to aid in data interpretation for both workflows. While METABOLIC was designed with environmental microbiomes in mind, it can also be applied to human microbiomes. This freely available tool should facilitate the integration of uncultivated microbial metabolisms into ecosystem metabolic and biogeochemical models.