Agriculture is practiced on 38% of the landmass on Earth, and having replaced natural ecosystems, it is the largest terrestrial biome on Earth. Agricultural biomes are typically focused on annual crops that are produced as a succession of genetically uniform monocultures. Compared to the ecosystems they replaced, agroecosystems provide fewer ecosystem functions and contain much less biodiversity. The large-scale conversion from natural lands to agriculture occurred centuries ago in the Old World (Africa, China, Europe, and India), but in many areas during the latter 20th and early 21st centuries, especially tropical areas with rich biodiversity, agriculture is an emerging industry. Here, displacement of natural ecosystems is also a late 20th-century occurrence, and much of it is ongoing. Regardless of where or when agriculture was established, biodiversity declined and ecosystem services were eroded. Agricultural practices are the second largest contributor to biodiversity loss, due to the loss of habitat, competition for resources, and pesticide use. Most (~96%) of the land used to produce crops is farmed using conventional methods, while smaller percentages are under organic production (~2%) or are producing biotech crops (~4%). Regardless of how agriculture is practiced, it exacts a toll on biodiversity and ecosystem services. While organic agriculture embraces many ecological principals in producing food, it fails to recognize the value of biotechnology as a tool to reduce the environmental impact of agriculture. Herbicide- and/or insect-resistant crops are the most widely planted biotech crops worldwide. Biotech crops in general, but especially insect-resistant crops, reduce pesticide use and increase biodiversity. The widespread adoption of glyphosate-resistant crops increased the use of this herbicide, and resistance evolved in weeds. On the other hand, glyphosate has less environmental impacts than other herbicides. Because of the limited scale of biotech production, it will not have large impacts on mitigating the effects of agriculture on biodiversity and ecosystem services. To have any hope of reducing the environmental impact of agriculture, agro-ecology principals and biotechnology will need to be incorporated. Monetizing biodiversity and ecosystem services through incorporation into commodity prices will incentivize producers to be part of the biodiversity solution. A multi-level biodiversity certification is proposed that is a composite score of the biodiversity and ecosystem services of an individual farm and the growing region were the food is produced. Such a system would add value to the products from farms and ranches proportionate to the level by which their farm and region provides biodiversity and ecosystem services as the natural ecosystem it replaced.