Old paper and leather are particularly vulnerable to physical and chemical degradation caused by fungus, due to their nature, which is primarily made up of natural materials. Synthetic fungicides, which have the potential to be hazardous to both human health and the environment, are the main target of the treatments typically used to preserve old paper and leather. Natural products, which are safe for the environment and have no negative effects on human health, have been widely advocated as an alternative to conventional antifungals. Pinus rigida wood extract was prepared in the current study at concentrations of 0.25%, 0.5%, and 1%. These extract concentrations were applied to model reference leather samples and generated cotton paper that was similar to the reported historical text. For the bioassay, the three most important fungi, Aspergillus flavus, Aspergillus niger, and Fusarium culmorum, were employed. HPLC was used to identify the phenolic and flavonoid components in this extract. The results showed that leather treated with 1% extract and 0.50%, measuring 5.33 mm and 3.33 mm, respectively, had the biggest inhibition zones (IZs) values against the growth of F. culmorum. A. flavus growth was not inhibited in paper or leather samples treated with the tested extract concentrations. The maximum IZ (6.66 mm) against the development of A. niger was seen in paper and leather samples treated with the extract at 1%. Cinnamic acid, caffeic acid, and benzoic acid were the main phenolic compounds in the methanol extract from Pinus rigida wood, with concentrations of 11.26, 8.11, and 4.23 µg/g, respectively. Quercetin, luteolin, and catechin were the main flavonoid compounds, with percentages of 12.39, 13.47, and 15.41 µg/g, respectively. This study offers an illustration of the true scientific procedures that proposed treating old historical manuscripts made of leather and paper with an environmentally friendly method.