Modern industrial agriculture is largely responsible for environmental problems, such as biodiversity loss, soil degradation, and alteration of biogeochemical cycles or greenhouse gas emission. Agroecology, as a scientific discipline as well as an agricultural practice and movement, emerged as a response to these problems, with the goal to create a more sustainable agriculture. Another response was the emergence of permaculture, a design system based on design principles, as well as a framework for the methods of ecosystem mimicry and complex system optimization. Its emphasis, being on a conscious design of agroecosystems, is the major difference to other alternative agricultural approaches. Agroecology has been a scientific discipline for a few decades already, but only recently have design principles for the reorganization of faming systems been formulated, whereas permaculture practitioners have long been using design principles without them ever being scrutinized. Here, we review the scientific literature to evaluate the scientific basis for the design principles proposed by permaculture co-originator, David Holmgren. Scientific evidence for all twelve principles will be presented. Even though permaculture principles describing the structure of favorable agroecosystems were quite similar to the agroecological approach, permaculture in addition provides principles to guide the design, implementation, and maintenance of resilient agroecological systems.