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Background: <i>Salmonella enterica</i> represents a considerable public concern worldwide, with farm animals often recognised as an important reservoir. This study gives an overview of the prevalence and serotype diversity of <i>Salmonella</i> over a 5-year period in the meat production chain in Estonia. Data on human salmonellosis over the same period are provided. Methods: <i>Salmonella</i> surveillance data from 2016 to 2020 were analysed. Results: The prevalence of <i>Salmonella</i> at the farm level was 27.7%, 3.3% and 0.1% for fattening pigs, cattle and poultry, respectively. <i>S</i>. Derby was the most prevalent serotype at the farm level for fattening pigs and <i>S</i>. Dublin for cattle. The top three serotypes isolated at the slaughterhouse and meat cutting levels were <i>S</i>. Derby, monophasic <i>S</i>. Typhimurium and <i>S</i>. Typhimurium with proportions of 64.7%, 9.4% and 7.0%, respectively. These serotypes were the top five most common <i>Salmonella</i> serotypes responsible for human infections in Estonia. <i>S</i>. Enteritidis is the main cause (46.9%) of human salmonellosis cases in Estonia, but in recent years, Enteritidis has not been detected at the slaughterhouse or meat cutting level. Conclusion: In recent years, monophasic <i>S</i>. Typhimurium has become epidemiologically more important in Estonia, with the second-highest cause in human cases and third-highest among the most prevalent serotypes of <i>Salmonella enterica</i> in the meat chain.