In the present study, Acacia saligna (Labill.) H.L.Wendl. wood blocks with dimensions of 0.5 × 1 × 2 cm were inoculated with five molds (Aspergillus niger, A. flavus, Alternaria tenuissima, Fusarium culmorum, and Trichoderma harzianum) and the changes in the organic acids (oxalic, citric, tartaric, succinic, glutaric, acetic, propionic, and butyric) of powdered wood were analyzed by HPLC. The effects of the five inoculated fungi on the alterations to the wood cell wall ultrastructures were examined by TEM. The wood became more acidic as it was inoculated with the studied fungi. From the HPLC analysis, the oxalic acid (293.34 µg/g o.d.) in the A. saligna, A. tenuissima (167.33 µg/g o.d.), and T. harzianum (245.01 µg/g o.d.) wood decreased, but it increased in the A. flavus (362.08 µg/g o.d.), A. niger (1202.53 µg/g o.d.), and F. culmorum (431.85 µg/g o.d.) inoculated wood. Citric acid was observed in the wood inoculated with A. flavus (110 µg/g o.d) and A. niger (2499.63 µg/g o.d). Tartaric (1150.98 µg/g o.d), acetic (2.04 µg/g o.d), and propionic (1.79 µg/g o.d) acids were found in the wood inoculated with A. niger. Butyric acid was found in small amounts. A loss of wood substances appeared as the electron-lucent increased in the middle lamella and the layers of the secondary wall. Within the secondary cell wall regions, checks and splits were also noted, which resulted from the effects of the acids on the carbohydrates, according to the fungus type and the acids. In conclusion, increasing the amount of organic acids in the wood samples through inoculation with fungi results in more degradations in the wood, especially in the wood inoculated with A. niger.