One of crucial waste management problems is the management of organic waste. This activity employs the composting. In case of green waste, its application seems reasonable, whereas the use of selected mixed waste raises problems related to the compost quality. Across countries, the non-sterile organic fraction of municipal solid waste is being separated through the mechanical-biological treatment. The technology is a solution of waste treatment and meets objectives set out in the Landfill Directive. There are many problems associated with the use of output products. The use of compost as a fertilizer requires determination of its impact on the environment. Compost quality can be assessed using analytical methods and phytotoxicity tests. Therefore, the aim of this study was to describe changes in physico-chemical, enzymatic, phytotoxicity and vegetation parameters occurring in composts from two systems - a prismatic installation for green waste, and a mechanical-biological treatment installation. The compost from green waste exhibited greater stability. Values of dehydrogenase activity were lower if compared with the mechanically and biologically treated compost, which indicates lower compost maturity. The biomass production of Brassica napus L. and Fetuca rubra L. was higher in the variant with the application of green compost. The influence on Hordeum vulgare L., Cannabis sativa L., and Sinapis alba L. depended on the plant type and the compost used. Nevertheless, the compost from green waste was less toxic. The evidence from this study suggests that the mechanical-biological treatment had problems associated with the maturation and quality of the final product.