An on-farm assessment of impact of pre-germinated rice intensification on chemical and physical characteristics of subtropical soils was performed in an ecologically based production system in Southern Brazil. Three soil orders (Planosol, Gleysol and Histosol) with different intensity of pre-germinated rice production in the last 11 summer seasons (no-rice – reference areas, under natural vegetation; low – 1 to 4 seasons; medium – 5 to 8 seasons, high – 9 to 11 seasons) were evaluated regarding soil physical and chemical characteristics. In general, even using until 3.5 Mg ha−1 per rice season of organic compost (32% C) in ecologically based rice production, the intensification of pre-germinated rice promoted soil degradation. Histosols were more susceptible to degradation, while Gleysols and Planosols had few soil characteristics influenced by rice cultivation. In comparison to soil under native vegetation, Histosols show losses of 75% of CEC, 33% of porosity, 70% of C and N stocks, 85% and 45% of available P and K, respectively. Our findings show that, even under flooding for half of year, this type of soil, soils under pre-germinated rice production show some degradation in this subtropical ecosystem, even under an ecologically based production system. In these environments, a low intensity of rice production should be performed aiming to avoid soil degradation at high rates. However, aiming to increase the income to farmers, the increase of crop residues input by use of cover crops or pastures in winter may be a feasible management for maintenance soil C and N stocks and nutrient cycling under more intense pre-germinated rice production systems in Southern Brazil.