The global demand for safe and healthy food with minimal synthetic preservatives is continuously increasing. Some natural food antimicrobials with strong antimicrobial activity and low toxicity have been considered as alternatives for current commercial food preservatives. Nonetheless, these natural food antimicrobials are hardly applied directly to food products due to issues such as food flavor or bioavailability. Recent advances in microencapsulation technology have the potential to provide stable systems for these natural antibacterials, which can then be used directly in food matrices. In this review, we focus on the application of encapsulated natural antimicrobial agents, such as essential oils, plant extracts, bacteriocins, etc., as potential food preservatives to extend the shelf-life of food products. The advantages and drawbacks of the mainly used encapsulation methods, such as molecular inclusion, spray drying, coacervation, emulsification, supercritical antisolvent precipitation and liposome and alginate microbeads, are discussed. Meanwhile, the main current applications of encapsulated antimicrobials in various food products, such as meat, dairy and cereal products for controlling microbial growth, are presented.