Ready-to-eat minimally processed fruits and vegetables are an ideal substrate for the growth of microorganisms, including human pathogens and mycotoxin-producing species, which questions about their quality and safety for customers. While we are aware of the importance of production workflows in structuring the products’ microbial communities, we still know little about the factors that shape microbiomes during the timeframe products are available to customers, and beyond this timeframe. Here, we study the influence of storage light condition (light or dark) on microbiological and physico-chemical parameters of minimally processed rocket leaves at different shelf life timepoints (day the product becomes available to consumers, expiration date, three days after the expiration date). Our results suggest that the total microbial load increases from the day the product becomes available to consumers, to the expiry date, and after the product’s expiration. However, when studying the composition of the fungal microbiome, we did not observe significant changes in its structure as effect of product shelf life or storage light condition. We also found that products stored under light condition had a higher total bacterial load compared to those stored in darkness. Our results might be helpful in crafting improved workflows for product’s storage during its shelf life, which might ultimately lead to a re-evaluation of storage times resulting in reduced food waste due to product spoilage or expiration.