In this article, rigid polyurethane foams obtained with the addition of a bio-polyol from rapeseed oil, were modified with the dimethyl propane phosphonate as additive flame retardant and two reactive flame retardants diethyl (hydroxymethyl)phosphonate and diethyl bis-(2-hydroxyethyl)-aminomethylphosphonate. The influence of used flame retardants on the foaming process and characteristic processing times of tested polyurethane systems were determined. The obtained foams were tested in terms of cell structure, physical and mechanical properties, as well as flammability. Modified foams had worse mechanical and thermal insulation properties, caused by lower cellular density and higher anisotropy coefficient in the cross-section parallel to the foam rise direction, compared to unmodified foam. However, the thermal conductivity of all tested foam materials was lower than 25.82 mW/m∙K. The applied modifiers effectively reduced the flammability of rigid polyurethane foams, among others, increasing the oxygen index above 21.4 vol.%, reducing the total heat released by about 41–51% and the rate of heat release by about 2–52%. A correlation between the limiting oxygen index values and both total heat released parameters from the pyrolysis combustion flow calorimetry and cone calorimetry was observed. The correlation was also visible between the value of the heat release capacity (HRC) parameter obtained from the pyrolysis combustion flow calorimetry and the maximum average rate of heat emission (MARHE) from the cone calorimeter test.