Composites containing natural fibers are considered environmentally friendly materials which is related to the reduced use of fossil fuels and the emission of carbon dioxide compared to petroleum-based polymers. Nevertheless, a complete evaluation of their environmental impact requires a broader view. This paper presents a carbon, ecological, and water footprints assessment of polypropylene-based composites filled with cotton, jute, and kenaf fibers based on a standardized European pallet (EUR-pallet) case study. Obtained results were compared with unmodified polypropylene and composite with glass fibers. Incorporation of 30 wt% of cotton, jute, and kenaf fibers into a polypropylene matrix reduced its carbon footprint by 3%, 18%, and 18%, respectively. Regarding the ecological footprint, an 8.2% and 9.4% reduction for jute and kenaf fibers were noted, while for cotton fibers, its value increased by 52%. For these footprints, the use of jute and kenaf fibers was more beneficial than glass fibers. Nevertheless, the application of natural fibers caused a 286%, 758%, and 891% drastic increase of water footprint of the final product, which was mainly affected by cultivation and irrigation of crops. Therefore, in a holistic view, the incorporation of natural fibers into the polypropylene matrix definitely cannot be impartially considered as an environmentally friendly solution.