Agriculture plays a major role on society, especially in developing countries which rely on commodity exportation markets. To maintain high crop productivity, the use of agrochemicals was once employed as the main strategy, which in turn affected soil, water, and human health. In order to aid this issue, identifying some alternatives, such as the implementation of biofertilizers and inoculants as bioinputs in modern agriculture, are imperative to improve ecosystem quality. Among these bioinputs, a few bioproducts have shown good performances, such as phytohormones (e.g., auxins and giberellins), biosurfactants, and other enzymes; thus, it is extremely important to assure the quality and feasibility of their production in biorefinery scenarios. These bioproducts can be synthesized through fermentation processes through utilizing plant biomasses and agricultural byproducts as carbon sources. In this sense, to increase the tecno-economical availability of these processes, the implementation of solid-state fermentation (SSF) has shown great potential due to its ease of operation and cost-attractiveness. Therefore, this study aims to describe the main substrates used in SSF systems for the production of potential bioinputs; their associated operation hurdles, parameters, and conditions selection; the most suitable microorganisms; and the underlying mechanisms of these molecules in soil dynamics. Within this context, this study is expected to contribute to the development of new processes in modern biorefineries and to the mitigation of environmental impacts.