The aim of this study was to identify the nature and cause of foxing spots in a historical manuscript. This manuscript was a Holy Quran from the beginning of the Qajar period and the end of the 18th century. Samples were incubated for 14 days and were evaluated for the presence of fungal activity. UV fluorescence photography, micro X-ray fluorescence spectroscopy and Fourier transform infrared spectroscopy were also used to investigate the characteristics and causes of foxing spots. The results showed that there was no fungal activity in the foxing spots of this manuscript. Based on the morphology of the stain in UV fluorescence photography, these foxing stains are of the Bullseye type, usually associated with metal ions. µXRF spectroscopy also showed a high accumulation of iron and copper at the site of these spots. This indicates abiotic foxing in this manuscript. Based on FTIR spectroscopy and peak deconvolution and fitting by Gaussian function, abiotic foxing increases the cellulose oxidation rate. Intensification of cellulose oxidation in foxing stains can be considered as one of the reasons for paper discoloration.