The development of a wound dressing with antibacterial properties and excellent exudate absorption capacity, while maintaining its structural integrity, is essential for preventing infections and ensuring a moist wound environment. This environment is crucial for enhancing the healing process and improving overall wound care effectiveness. In this study, we created a multifunctional bilayer (hydrogel/sponge) nanocomposite as a wound dressing material. The hydrogel layer is made from sodium alginate enriched with Sambucus ebulus plant extract, which is a natural and environmentally friendly resource. This extract provides both antibacterial and antioxidant benefits. The sponge layer is composed of the mucilage from Alyssum homalocarpum seeds, combined with zinc oxide nanoparticles to enhance its absorption ability, mechanical properties, and antibacterial function. This mucilage offers a promising and sustainable alternative to synthetic polymers. We evaluated the characteristics of the fabricated bilayer nanocomposite using various techniques, including contact angle measurement, liquid absorption analysis, porosity assessment, water retention testing, and water vapor transmission rate determination. Additionally, we conducted biochemical tests, such as blood clotting assessment, compatibility analysis, cytotoxicity evaluation, biodegradability testing, free radical scavenging assays, and antibacterial tests, to determine the applicability of the multifunctional bilayer nanocomposite. The results indicate that this multifunctional bilayer nanocomposite possesses not only suitable mechanical, absorption, and antibacterial properties but also effectively maintains an optimal wound environment, significantly enhancing the healing process. Furthermore, it reduces reliance on synthetic materials, paving the way for more environmentally friendly solutions in wound care applications. Ultimately, this approach promotes better health outcomes while minimizing environmental impact.