Organic agriculture has expanded in many countries to encourage the consumption of safe food for human health and to rejuvenate agroecosystems in the surrounding environment. Agricultural inputs for organic agriculture must be based on scientific investigations, as bioproducts can be substituted for agrochemicals, leading to modern organic agriculture. Microbial biotechnology in agriculture has attracted increasing attention as an important strategy for developmental sustainability. The innovation of this research is the identification of new effective microbes for microbial fermentation, plant growth promotion, disease control, insect protection, and weed control, including integrated management, which can contribute to modern organic agriculture toward sustainable development goals (SDGs). Agricultural inputs for organic agriculture are key for crop and animal productivity and can be used as substitutes for agrochemicals, resulting in equal yields in terms of quality and quantity. Modern organic agriculture has been proposed as an improvement over traditional organic agriculture. Organic certification is required for organic products and foods to ensure that they are free from toxic agrochemicals and harmful human pathogens such as Salmonella spp. and Escherichia coli, and that they contain low levels of nitrates and heavy metals. Based on scientific findings, the use of agricultural inputs such as microbial decomposers, microbial fertilizers, microbial fungicides, microbial insecticides, and microbes for heavy metal remediation is proposed to support successful organic production of vegetables, fruits, and other crops in compliance with organic certification standards.