Stored fish are frequently contaminated by foodborne pathogens. Lipid oxidation and microbial growth during storage are also important factors in the shelf-life of fresh fish. In order to ensure the safety of fish items, there is a need for control measures which are effective through natural inhibitory antimicrobials. It is also necessary to determine the efficacy of these products for fish protection against oxidative damage, to avoid deleterious changes and loss of commercial and nutritional value. Some synthetic chemicals used as preservatives have been reported to cause harmful effects to the environment and the consumers. The present investigation reports on the extraction by hydrodistillation and the chemical composition of three citrus peel essential oils (EOs): orange (Citrus sinensis L.), lemon (Citrus limonum L.) and bergamot (Citrus aurantium L.) from Algeria. Yields for EOs were between 0.50% and 0.70%. The chemical composition of these EOs was determined by gas chromatography coupled with mass spectrometry (GC/MS). The results showed that the studied oils are made up mainly of limonene (77.37%) for orange essential oil (EO); linalyl acetate (37.28%), linalool (23.36%), for bergamot EO; and finally limonene (51.39%), β-pinene (17.04%) and γ-terpinene (13.46%) for lemon EO. The in vitro antimicrobial activity of the EOs was evaluated against Staphylococcus aureus (S. aureus) using the agar diffusion technique. Results revealed that lemon EO had more antibacterial effects than that from other EOs. Minimal inhibitory concentrations (MICs) showed a range of 0.25–0.40 μL/mL. Lemon and bergamot citrus peel EOs were added at 1 × MIC and 4 × MIC values to Sardina pilchardus (S. pilchardus) experimentally inoculated with S. aureus at a level of 3.5 log10 CFU/g and stored at 8 ± 1 °C. The results obtained revealed that the 4 × MIC value of bergamot reduced completely the growth of S. aureus from day 2 until the end of storage. The presence of EOs significantly extended lipid stability. Samples treated with bergamot EO displayed greater antioxidant activity than lemon EO. In fact, the oxidation rate is inversely proportional to the concentration of EO. At 1 × MIC and 4 × MIC values of bergamot EO, the levels of malonaldehyde compared to the control samples were 1.66 and 1.28 mg malonaldehyde/kg at the end of storage, corresponding to inhibition percentages of 42.76% and 55.87%, respectively. These results suggest the possibility that citrus EOs could be used as a way of combating the growth of common causes of food poisoning and used as potent natural preservatives to contribute to the reduction of lipid oxidation in sardines.