Postharvest loss is a serious problem in Nigeria and a major drawback towards food security. Hence, discovery of potential agents capable of minimizing postharvest loss is urgently needed. This research is directed at investigating the in vivo antimicrobial activity of essential oils against bacterial pathogens isolated from Ipomoea batatas Lam. Citrus sinensis (sweet orange) and Citrus limon (lemon) peels and Zingiber officinale (ginger) essential oils were extracted using hydro-distillation and their chemical constituents determined by gas chromatography mass spectrometry (GC-MS). Morphological and biochemical methods were employed for bacterial identification. A total of 22 terpenes were identified with Citrus sinensis comprising of 13 monoterpenes, 8 sesquiterpenes and 1 diterpene. Citrus limon had 31 terpenes 15 of which are monoterpenes, 15 sesquiterpenes and 1 diterpene while a total of 30 terpenes were identified with Zingiber officinale comprising of 12 monoterpenes and 18 sesquiterpenes. Three of the four isolated bacteria identified from Hannah sweet potato were pathogenic: Erwinia carotovora, Bacillus licheniformis and Pseudomonas fluorescens. Pseudomonas fluorescens was more sensitivity to the essential oils at (p≤0.05). Citrus sinensis (64.29%) was three fold more active than Citrus limon (21.43%), while Zingiber officinale (53.57%) was two and a half fold more active than Citrus limon. Results obtained in this study showed that essential oils extracted from Citrus sinensis and Zingiber officinale exhibited substantial antimicrobial activity against bacterial induced sweet potato rot. Therefore, essential oils extracted from Zingiber officinale and Citrus sinensis could be used to control postharvest bacteria induced rots in injured sweet potatoes.