Background: This study evaluated the antimicrobial potentials of Citrus essential oils (CEOs) against spoilage microorganisms isolated from selected fruits. The fruits were randomly purchased from different markets in Akure, Nigeria. Methods: The microorganisms were isolated and identified using molecular tools. In vitro antimicrobial efficacies of CEOs and their synergistic potentials were tested against spoilage microorganisms using agar well diffusion. The bioactive compounds in CEOs were identified using gas chromatography-mass spectrometry (GC-MS). Results: The highest bacterial count (5.84 × 10 5 cfu/g) was recorded in tomatoes, while African star apple had the highest fungal count of 3.04 × 10 5 sfu/g. Microorganisms isolated from fruits were Bacillus spp., Micrococcus luteus, Serratia marcescens, Aspergillus spp., Mucor piriformis, Fusarium oxysporum, Penicillium spp., Rhizopus spp., Alternaria alternata and others. Phytochemicals in the CEOs were anthraquinones, cardiac glycosides, tannins, alkaloids, terpenoids, saponins, steroids, flavonoids and phenol. The diameter zones of inhibition displayed by CEOs against tested microorganisms at 100 mg/ml ranged from 3.3 mm to 26.8 mm with B. muralis being the most susceptible bacteria. The minimum inhibitory concentration (MIC) against all the tested isolates ranged from 12.5 to 100 mg/ml, while the minimum bactericidal and fungicidal concentrations ranged from 25 to ≥ 100 mg/ml. The synergism between lime and lemon at ratio 1:1 had better antimicrobial activity than each essential oil when used singly. GC-MS revealed the presence of limonene, beta-pinene, alpha-phellandrene, terpinen-4-ol, alpha-terpineol and geraniol in EOs of lime and lemon. Conclusion: The inhibitory potential of CEOs could be attributed to their bioactive compounds, which can be exploited and used as preservatives by food industries.