Cropping system diversification can reduce the negative environmental impacts of agricultural production, including soil erosion and nutrient discharge. Less is known about how diversification affects energy use, climate change, and air quality, when considering farm operations and supply chain activities. We conducted a life cycle study using measurements from a nine-year Iowa field experiment to estimate fossil energy (FE) use, greenhouse gas (GHG) emissions, PM2.5-related emissions, human health impacts, and other agronomic and economic metrics of contrasting crop rotation systems and herbicide regimes. Rotation systems consisted of 2-year corn-soybean, 3-year corn-soybean-oat/clover, and 4-year corn-soybean-oat/alfalfa-alfalfa systems. Each was managed with conventional and low-herbicide treatments. FE consumption was 56% and 64% lower in the 3-year and 4-year rotations than in the 2-year rotation, and GHG emissions were 54% and 64% lower. Diversification reduced combined monetized damages from GHG and PM2.5-related emissions by 42% and 57%. Herbicide treatment had no significant impact on environmental outcomes, while corn and soybean yields and whole-rotation economic returns improved significantly under diversification. Results suggest that diversification via shifting from conventional corn-soybean rotations to longer rotations with small grain and forage crops substantially reduced FE use, GHG emissions, and air quality damages, without compromising economic or agronomic performance.