The addition of functionalized materials (biochar, zeolite, and diatomite) and lyophilized metabolic products of Pseudomonas sp. and Bacillus subtilis to composted biomass may bring many technological and environmental benefits. In this study, we verify the effects of biochar, zeolite Na-P1 (Na6Si10Al6O32·12 H2O), diatomite (SiO2_nH2O), and bacterial metabolites on the composting of biomass prepared from poultry litter, corn straw, grass, leonardite, and brown coal. The experimental design included the following treatments: C—biomass without the addition of functionalized materials and bacterial metabolites, CB—biomass with the addition of biochar, CBM—biomass with the addition of biochar and bacterial metabolites, CZ—biomass with the addition of zeolite, CZM—biomass with the addition of zeolite and bacterial metabolites, CD—biomass with the addition of diatomite, and CDM—biomass with the addition of diatomite and bacterial metabolites. Composts were analyzed for enzymatic and respiratory activities, mobility of heavy metals, and the presence of parasites. The results of this study revealed that, among the analyzed functionalized materials, the addition of diatomite to the composted biomass (CD and CDM) resulted in the most effective immobilization of Cd, Zn, Pb, and Cu. Zinc immobilization factors (IFHM) for diatomite-amended composts averaged 30%. For copper, each functionalized material was found to enhance mobilization of the element in bioavailable forms; similar observations were made for lead, except for the compost to which biochar and bacterial metabolites were added (CBM). The determined values of biochemical indicators proved the different effects of the applied functionalized materials and bacterial metabolites on the microbial communities colonizing individual composts. The dehydrogenase activity (DhA) was lower in all combinations as compared with the control, indicating an intensification of the rate of processes in the studied composts. The highest basal respiration (BR) and substrate-induced respiration (SIR) activities were determined in composts with the addition of bacterial metabolites (CBM, CZM, and CDM). The addition of functionalized materials completely inactivated Eimeria sp. in all combinations. In the case of Capillaria sp., complete inactivation was recorded for the combination with zeolite as well as biochar and diatomite without bacterial metabolites (CB, CZ, and CD).