As a result of the Kakhovka dam explosion, a huge area of soil was contaminated with toxic organic waste of various origins. The sustainability of soil ecosystems affected by floods requires effective approaches to eliminate the consequences as quickly as possible. Therefore, the goal of this work was to study the efficiency of the application of granular microbial preparation (GMP) and silicon dioxide preparation Analcime for the degradation of toxic organic waste to restore the soil after floods as well as man-made and natural disasters using model ecosystems. It is based on the combination of microbial fermentation of organic waste via GMP, improvement in soil quality via silicon dioxide preparation Analcime (Na[AlSi2O6 ]·H2O), followed by the application of phytoremediation methods for affected soil bioremediation. Such parameters as time detention (Td) and degradation coefficient (Dc) served to estimate the efficiency of organic waste degradation. The detoxification efficiency was determined via growth inhibition coefficients of indicator plants. The coefficient of waste degradation (Dc) via GMP was four–eight-fold higher compared to untreated variants and ranged from 35.1 to 41.8. The presence of methane in the variants of the experiment with GMP indicated the complete degradation of solid waste to final non-toxic products. The addition of GMP and Analcime enhanced the viability and antioxidant protection systems of seedlings of test plants (Cucumis sativus «Konkurent» and Amaranthus caudatus L.). The proposed approach is promising to be applied in the polluted sites of Europe or Asia for soil treatment as well as alternative energy obtaining