Among different organic fillers, the chemical composition of Syzygium aromaticum, commonly known as cloves, has great potential as a sustainable reinforcement for polymeric materials. In the study, grounded cloves were used as cellulosic filler for a novel polyurethane (PU) composite foams. Soybean oil-based PU composite foams were successfully reinforced with different concentrations (1, 2, and 5 wt%) of clove filler. PU foams were examined by rheological behavior, processing parameters, cellular structure (scanning electron microscopy analysis), mechanical properties (compression test, impact test, three-point bending test), thermal properties (thermogravimetric analysis), viscoelastic behavior (dynamic mechanical analysis) as well as selected application properties (apparent density, dimensional stability, surface hydrophobicity, water absorption, color characteristic). In order to undertake the disc diffusion method, all PU composites were tested against selected bacteria (Escherichia coli and Staphylococcus aureus). Based on the results, it can be concluded that the addition of 1 and 2 wt% of clove filler leads to PU composite foams with improved compression strength (improvement by ≈18% for sample PU-1), greater flexural strength (increase of ≈11%), and improved impact strength (increase of ≈8%). Moreover, it has been proved that clove filler may be used as a natural anti-aging compound for polymeric materials. Based on the antibacterial results, it has been shown that the addition of clove filler significantly improved the antibacterial properties of PU foams and is suitable for the manufacturing of antimicrobial PU composite foams. Due to these positive and beneficial effects, it can be stated that the use of cloves as a natural filler in PU composite foams can promote a new application path in converting agricultural waste into useful resources for creating a new class of green materials.