Polyurethane foams are a versatile class of polymeric materials whose physico-chemical structure and properties can be modified by incorporating additives. This study examined the effect of naturally occurring insect-repelling additives such as neem oil (NO) and clove powder (CP) on the formulation and morphology of flexible polyurethane foam (FPUF) composites. The foams were prepared by the prepolymer method using a box test as applied in the foam industry. The composite material was formulated by varying the isocyanate index (103 and 108) as an excess amount of isocyanate was required to react with the additives. The formulation at 103 was unsuccessful as the foams collapsed immediately after rising. However, at 108, two main categories of foams were successfully prepared: foams containing either NO or CP and the other containing both additives. The effect of these additives on the formulation was examined by monitoring the foam reaction using the cream, tack-free, and rising times. It was observed that the cream, tack-free, and rising times increased with increasing NO/CP content. Conversely, the morphology was studied using scanning electron microscopy (SEM) and optical microscope (OP). The SEM images revealed disruption of the foam network with 1 wt% NO, likewise those containing 1 wt% CP. The cellular network of the foams with simultaneous addition of NO and CP was similar to that of the neat foams and had no broken cell joints and struts due to better dispersion of the additives in the polyurethane matrix. The study indicates that the combined addition of NO and CP modifies the morphology of FPUF, which can influence their physico-mechanical properties.