In the present study, Melia azedarach wood blocks treated with different acetone extract concentrations from Withania somnifera fruits are assessed for their antibacterial and anti-fungal activities. Wood blocks of M. azedarach treated with W. somnifera fruit extract at concentrations of 0, 1, 2, and 3% are evaluated for in vitro antimicrobial activity against five genbank accessioned bacterial strains—Agrobacterium tumefaciens, Dickeya solani, Erwinia amylovora, Pseudomonas cichorii, and Serratia pylumthica—and two fungi, namely, Fusarium culmorum and Rhizoctonia solani. Through HPLC analysis we find that the most abundant quantified phenolic and flavonoid compounds of acetone extract (mg/100 g) are salicylic acid (9.49), vanillic acid (4.78), rutin (4702.58), and myricetin (1386.62). Wood treated with the extract at 2% and 3% show no growth of A. tumefaciens, E. amylovora, and P. cichorii. Use of the extract at 3% causes inhibition of fungal mycelia of F. culmorum and R. solani by 84.07% and 67.03%, respectively. In conclusion, potent antifungal and antibacterial activity against plant pathogens is found when an acetone extract of W. somnifera fruits is applied to wood samples.