Methods and systems for generating agronomic indices and executing one or more actions in response to said agronomic indices at an agriculture site, the method comprising: receiving a set of samples associated with the agriculture site; generating a sample dataset upon processing the set of samples with a set of sample processing operations; generating a set of microbiome-associated features upon performing a set of transformation operations upon the sample dataset, wherein the set of microbiome-associated features comprises a first subset of taxonomic annotations, a second subset of functional annotations and a third subset of ecological indices; generating values of a set of agronomic indices based upon the set of microbiome-associated features; and executing an action for producing a desired outcome at the agriculture site, based upon the set of agronomic indices.