Interfacial properties, crystallinity and flammability of short fiber reinforced and flame retarded polyamide 6 and polyamide 66 compounds are investigated, emphasizing the influence of flame retardant fillers on the resistance of fiber/matrix interface to shear. Interfacial shear strengths are derived through a micromechanical approach by determining the tensile properties and residual fiber length distributions. Validated by fracture morphologies, interfacial strengths are found to be governed by filler-induced apparent crystallinities and fractional occurrence of polyamide polymorphs, obtained via peak deconvolution of X-Ray diffraction patterns. Although flame retardant additives based on Br/Sb synergism are found to impart excellent flammability reductions regarding oxygen index and UL94 classifications (V-0 rating), degree of crystallinity; thus, interfacial properties are deteriorated due to lowered thermal expansion and increased cooling rates. Red phosphorus as a flame retardant also induces a UL94 V-0 and significant reduction in flammability together with the facts that crystallinity is not altered and a strong fiber/matrix interface is maintained. Use of melamine cyanurate in an unreinforced polyamide improves the limiting oxygen index considerably; however, the UL94 rating remains unchanged as V-2 as a consequence of increased level of melt dripping. Melamine cyanurate additionally increases the degree of crystallinity through promotion of heterogeneous nucleation.