The effects of improved method of extraction on the physicochemical, mycological and stability of crude Canarium Schweinfurthii fruit oil were studied. The extracted oils were then stored at 25±5oC for 24 months with samples analyzed at 6months interval for; pH, saponification value, acid value, peroxide value and iodine number. Similarly, enumeration and identification of fungi species was determined using standard mycological procedures. The results showed that crude Canarium Schweinfurthii fruit oil obtained by the improved method of extraction had better quality and stability parameters than the traditional method extracted oil. At 24months the oil quality values of; pH 5.20 – 6.61, Acid value 0.53 – 1.02 (mg of KOH/g), saponification value 151.30 – 179.52 (mg of OH/g), peroxide value 0.031 – 1.500 (meq 02/Kg) and iodine value 85.02 – 101.60 (gI2/100g). Comparatively, no significant difference (P > 0.05) was observed for pH and saponification values for the extracted oils, with values of 6.60, 178.60(mg of OH/g) and 6.62, 178.52(mg of OH/g) for traditional and improved extraction methods respectively. During storage the oils showed average fungal counts of 00.00 to 1.72 x105 and 00.00 to 8.00 x104 CFU/ml oil at 0 and 24 month for traditional and improved methods extracted oils respectively. Predominant fungal species; Aspergillus niger, Rhizopus stolonifer, Sacccaromyces cerevisiae, Mucor spinosus, Penicillium patalun, Fusarium oxysprum and Candida scotti were found associated with the stored canarium oil. Generally, Mucor spinosus (80.00%), Aspergillus niger (80.00%) and Penicillium patalum (80.00%) had the highest occurrence in traditional extracted oil. This finding suggests the need for the local processors to reevaluate the full processing method in order to retain better fungal quality and oxidative stability for Canarium schweinfurthii fruit oil.Keywords: Canarium schweinfurthii, fruit oil, Extraction, Fungal Isolates, Oxidative stability