Metagenomics is a contemporary discipline in science that introduces a new horizon in biomolecular and genetic studies and provides a standard method for understanding biological diversity. In this context, we can only assess the functional potential of a certain community through metagenomics, but by understanding the metaphenomics, we can assign the functional genetic potential with respect to environmental resources. Metaphenomics studies the phenome of soil, plants or other organisms through a meta-analysis with the primary goal of establishing dose–response relationships across a wide range of phenotypic characteristics and abiotic environmental factors. Rather than conjecturing gene functions by metagenomes, the metaphenomic approaches can assist in understanding the substantial functioning of the microbiome. Coupling metagenomics with metaphenomics has the potential to overcome practical challenges in agriculture and ecological sustainability. On the grounds, this review was performed to present a deep understanding of soil metagenomics linked with metaphenomics, i.e. the phenotypic response of the soil microbiome. It also discusses how metagenomic applications and basic methods help study the phenotypic response of uncultured soil microbiomes to external factors. Metaphenomics can apply an untargeted multiomics approach to decipher the soil microbiome metaphenotypic response to environmental perturbations, and its application is also reviewed in this article.