Polyurethane–clay nanocomposite adhesives were prepared by different synthetic routes and their microstructures were determined by X-ray diffraction measurements and from transmission electron microscopy images. The preparation method of the polyurethane nanocomposite adhesives was systematically changed, that is, condensation either in the presence or absence of catalyst, concentration and type of nanoclay, premixing order of nanoclay (nanoclay was either premixed with the polyol or isocyanate part) and by using MDI surface treated nanoclays. Depending on the polymerization conditions cluster, intercalated, and exfoliated clay structures were obtained. The flame retardant properties of the manufactured nanocomposite adhesives and the synergistic effect of clay in combination with dolomite were investigated by cone calorimeter and UL 94 vertical burning tests. The results indicate that addition of nanoclay reduces burning time and the total heat evolved (THE) at flame out, and that the type of assembled clay structure (cluster, intercalated or exfoliated) had a significant effect on the flame retardant property. Nanocomposites with 3 wt % of clay loading gave the shortest burning time, the lowest THE and also UL 94 V-2 ratings were reached, although the flame retardancy in terms of heat release rate and time to ignition was not improved.