Coffee and soil have a idiosyncratic relationship with each other that can only be acquired through the presence of several specific factors which require varying external factors that impact conditions necessary for premium flavor, and minimal depletion impact. Much like the demands needed for proper Cacao growth, many principles can be assimilated with coffee, and in some cases both have interacted with each other. By diversifying local canopy providing trees which help regulate N, and Al levels can help with regulating soil temperatures and ultraviolet exposure.  Volcanic mineral toxicity as well as large-scale fertilizers, pesticides, and insecticide impact is also reversible to a degree with this effect. Tropical and Subtropical environments typically show heavily leached or oxidized soils which if not properly managed can lead to rapid depletion if used for agricultural production. The necessity of regulating Ca, K, Mg, and N for instance can heavily boost the quality in soils. By implementing a canopy structure with available host plants, support, or provider species, the accumulation and storage of organic matter, biota, and other biologic or chemical compounds can become utilized by root systems largely within the A horizon where the majority of Coffee roots benefit. Without this balanced structure in place or managed, the soils can easily revert to a more basic pH state, allowing less exchange between materials or matter. Through geoarchological analysis, the cultural management practiced by prehistoric Mesoamericans (as well as pockets of their modern descendants) involved annual organized slash & burn techniques which replenishes the soil through fortification from disease and pests. This activity can be seen both in the ethnographic record, and through the use of devices such as an infiltrometer to detect water ratios in soils and other determining factors in pyrogeography.

Flora and Fauna associated with coffee has been largely a knowledge reserved for indigenous, or traditional and family growers of small-scale operations that has been known to harbor an equilibrium in the production processes from seed to market. Within the last several decades however, extensive research and analysis from multidisciplinary perspectives have given promise to the well-being of coffee species related to the local flora. Nitrogen enriching trees such as various fruit bearing tropical varieties like Guava, Banana, and other local species that also double in providing shading canopies for temperature regulation. Through the promotion of provider species in direct adjacency to coffee shrubs, the biodiversity of birds, insects, and mammals has the potential to increase and stabilize at greater rates than when compared to the recent trend of mono-crop, sun grown operations. Butterfly populations and occurrences in particular, through the monitoring of natural behaviors have been linked to the vitality of ecosystems, favoring forest canopy and flora apart of biologically diverse ecosystems and landscapes. This has risen awareness over the debate of butterflies being an indicator species for malpractice, toxicity, or shrinking wildlife habitat. By understanding the sensitive requirements of indicator species with the native landscape, the relationship coffee has with complimentary flora for the development of its own requirements can be seen when biodiversity among the area is removed for sun grown production. The promotion of Epiphytes in particular, also has unique relationship with the potency of coffee yields by providing nutrients to host species, and harboring habitats for bacteria, funghi, and other support plants. If these processes are found in a balance, so too will the chances of higher grade cup quality at lesser impacts.