Biodegradable packaging, both alone and in combination with acid whey protein coatings, has been used to pack fresh Gouda cheese to improve preservation prior ripening or storage. This study involved three key components: (i) the selection of biodegradable packaging (BP), (ii) the development of a plain liquid acid whey protein concentrate, pectin-based edible coating (BP + Ch + Coating), and (iii) the incorporation of at least 6 log10 CFU (colony forming units) mL−1 Lacticaseibacillus paracasei (BP + Ch + Coating + Lp) and Lactobacillus helveticus (BP + Ch + Coating + Lh) strains. The created compositions were compared with cheese packed in conventional polyethylene (PE) packaging to evaluate their overall synergy effect in reducing microbiological spoilage and influencing chemical parameters in Gouda cheese during 45 days of ripening and cold storage. The evaluation included microbiological analysis (total LAB, Enterobacteriaceae spp., and fungi CFU) and quality assessment of pH, moisture content, water activity, texture, and colour (CEI system) during ripening and shelf life. Although biodegradable packaging (BP) alone did not protect the cheese effectively compared to conventional packaging (EVA/PE/EPC/PVDC), the combination of biodegradable packaging with a coating (BP + Ch + Coating) showed protective properties against Enterobacteriaceae spp. and mould, maintaining moisture, pH, and colour during ripening and storage. Incorporation of L. helveticus (BP + Ch + Coating + Lh) into the coating efficiently decreased the growth of fungi.