Soil fertility is the ability of a soil to sustain plant growth by providing essential plant nutrients and favorable chemical, physical, and biological characteristic as a habitat foe plant growth. Organic farming is a production system that excludes the use of artificially compounded fertilizers, pesticides, growth regulators, genetically modified organism, antibiotics and livestock feed additives. Soil health and quality is the foundation of organic farming and therefore maintenance of soil biological status is one of the important components in organic soil. Due to the regulations of organic farming, few options remain for organic farmers to manage pests and diseases in their crops compared to conventional farming. However, major pests could still be managed through manipulation of the agroecosystem processes in advantage of the crops and disadvantage of pests. The limited number of active plant protection substances authorized for use in organic farming can provide support to natural and biological control agents in suppression of pests and diseases. This chapter highlights the principles and strategies of soil fertility management and crop protection in organic farming.