Egg-associated salmonellosis is a major problem for food safety. It can be caused by vertical transmission (transovarian transmission) in hens and horizontal transmission though penetration. Despite a series of physical and chemical defense mechanisms naturally found in eggs, they cannot provide complete protection for them. Environmental hygiene, bacteria vectors such as birds, rodent, flies, and beetles along with feed and water contamination are the most frequently reported causes of Salmonella colonization in hens, and finally to eggs. In addition, inappropriate egg handling will cause eggs to lose their self-protection ability, thus resulting in the survival and multiplication of Salmonella in an egg's contents, which contributes to the horizontal dissemination. The routes of Salmonella contamination were discussed, and the effectiveness and shortcomings of different decontamination methods were evaluated in this review. Various studies on egg storage indicated that the low-temperature storage without temperature fluctuation was beneficial for the control of Salmonella. This review, based on an understanding of the stages of Salmonella transmission and an egg's self-protection mechanisms, highlights a comprehensive strategy toward Salmonella control in a process from egg production and handling to human consumption.