Local indigenous biodiversity has significantly declined. Beginning colonial times, governments and communities have cleared indigenous forests, converting them into farmlands that are planted with exotic varieties of crops, trees, shrubs, herbs and grasses. This significantly disrupts the natural ecological balance with adverse effects like decline in plant and animal species, sometimes leading to extinction.

Communities have changed their ways of life leading to decline in use of herbal medicine and indigenous foods which leads to far reaching health and nutritional consequences to the people, including disease and short life expectancy. Increase in soil erosion, use of chemical herbicides and fertilizers has resulted to environmental changes that destroy natural resources resulting to high levels of  food insecurity in naturally highly productive areas. Partly due to loss of biodiversity, Kenya is fast experiencing impacts of climate change.