By-products of animal breeding and raising can contain considerable amounts of trace elements, including Mn and Fe, due to the fact that their amounts in fodders are purposefully being increased. Thermal conversion of pig manure and poultry litter may have a significant effect on changes in the content and mobility of Mn and Fe in these materials. The aim of the research was to evaluate the effect of thermal conversion of pig manure and poultry litter on the content and mobility of Mn and Fe in biochars and in soil after their application (0.5%, 1%, and 2% amendments to the soil). As a result of thermal conversion of pig manure and poultry litter, an increase in the content of total forms and a reduction of Mn and Fe forms extracted with water were recorded. The 2% amendment of pig manure biochar to soil caused an increase in the content of mobile forms of Fe, whereas poultry litter biochar decreased mobility of this element. Introduction of pig manure biochar and poultry litter biochar to the soil caused a similar immobilization of mobile forms of Mn as in the case of application of thermally unprocessed manure and litter. It has been shown that the content of Fe and Mn extracted with 0.025 M C10H22N4O8 was higher than the content of these elements extracted with 1 M NH4NO3.