In developing countries, markets are the main supply of horticultural products to populations, but this can pose a public health challenge due to the risk of the fecal-oral transmission of gut pathogens. This transmission is strongly associated with inadequate public sanitation or low standards of personal and domestic hygiene, and their prevalence can cause gastrointestinal diseases, which are the third leading cause of death in Mozambique. This study aims at assessing the risk for public health of horticultural products supply chain, from the farmers-vendors to the consumers, in municipal markets in Maputo-City, Mozambique. Surveys (75) were conducted on vendors and an observational analysis was performed in the markets under study. The results showed that 62% of the vendors had access to water from boreholes or artisanal sources and the issue “access to water” was significantly different between markets (p = 0.004). Of the vendors who wash their products (53.3%), only 7.5% use tap-water for this purpose, with the difference in attitudes being statistically significant between vendors in the markets (p = 0.035). The majority (60.4%) said that vegetables and fruits can cause diseases due to pesticides and only 31.3% believe that the diseases may be related to poor hygiene. Despite the vendors’ low knowledge of Good Hygiene Practices (GHP), we noticed that women have better practical assimilation of GHP when compared to men (p = 0.008). Although Maputo’s markets are struggling to achieve quality hygiene standards in a reliable and sustainable manner, their resources are limited and significantly different (p = 0.044) from market to market, and this problem remains a concern for the public-health authorities of the city. In conclusion, the provision of adequate drinking water and sewage disposal systems, together with education for health of vendors, can reduce the risk of contamination of fresh food by the more common organisms causing diarrhea in children, including intestinal parasites.