The use of natural preservatives in the storage of fresh fruits is a promising approach to healthier and more sustainable food processing. The current study was conducted to evaluate the effect of pomegranate peel extract (PPE) and lactic acid (LA) as natural preservatives on the shelf life of Khalal Barhi date fruits. Physicochemical properties, antioxidant activity, color parameters, texture profile, sensory characteristics, and microbiological quality of date fruits were evaluated during six weeks of cold storage (4 ± 1 °C). The bioactive compounds in PPE were determined by HPLC analysis, which showed that PPE is a rich source of bioactive compounds, particularly phenolics and flavonoids. The results exhibited decreased moisture content (from 68.36–68.43 to 62.13–63.11%) and an increased soluble solids content (from 27.16–27.24 to 31.45–33.91%) in all samples with prolonged storage. Likewise, a slight decrease in the pH (from 6.00–6.28 to 4.89–5.29) with an increase in acidity (from 0.12–0.14 to 0.23–0.27%) during storage was observed. Generally, treated samples showed lower changes in moisture content, soluble solids content, pH, and acidity than the control. A decrease in total phenolic content (TPC) (from 8.22–12.36 to 3.19–5.17 mg GAE/g) and antioxidant activity (from 44.11–68.26 to 23.84–38.52%) of all samples was observed with progressed storage, meanwhile, the treatment with PPE significantly (p < 0.05) increased TPC with a concomitant increase in antioxidant activity and maintained higher values of both throughout storage. The results exhibited a decrease in L* (from 54.87–55.92 to 41.68–45.68) and b* (from 36.25–37.09 to 23.59–25.42) values of all samples, while the a* value of all samples increased (from 1.29–1.40 to 2.22–2.43) with storage. Dipping treatment in PPE solution improved the color, exhibited the lowest change in color parameters, and maintained better texture properties during storage. Similarly, sensory properties decreased (from 8.21–8.66 to 6.71–7.21) during storage with insignificant (p > 0.05) differences among samples. Dipping treatments inhibited the growth of yeasts and molds over time, with the lowest microbial count recorded in the PPE-treated samples. It can be concluded that PPE was found to have protective effects on Khalal Barhi date fruit quality by controlling post-harvest changes and lowering the microbial load.