The aim of the research was to investigate the influence of calcium phosphinate (HPCA) and aluminum phosphinate (HPAL) in synergistic systems with organophosphorus compounds, i.e., diphenylcresyl phosphate (CDP) and trichloropropyl phosphate (TCPP), on the thermal stability, flammability, smoke density, and emission of toxic gases during the thermal decomposition of polyurethane (PUR) foams. Thermogravimetric analysis (TGA), along with cone calorimetry and microcalorimetry, were used to assess the influence of fillers on the thermal stability and flammability of PUR foams. The analysis of toxic gas products was performed with the use of a coupled TG–gas analyzer system. The optical density of gases was measured with the use of a smoke density chamber (SDC). The obtained results showed an increase in thermal stability and a decrease in the flammability of the PUR composites. However, the results regarding smoke and gas emissions, as well as toxic combustion by-products, present ambiguity. On one hand, the applied flame retardant systems in the form of PUR-HPCA-CDP and PUR-HPCA-TCPP led to a reduction in the concentration of CO and HCN in the gas by-products. On the other hand, they clearly increased the concentration of CO2, NOx, and smoke emissions. Microbiological studies indicated that the obtained foam material is completely safe for use and does not exhibit biocidal properties.