Bacterial foodborne diseases are one of the most important public health issues worldwide but in Ecuador reports on the microbiological quality of foods are scarce. In this cross-sectional study, a total of 450 samples of high-demand Ecuadorian food, including bolon, encebollado, sauces, ceviche, fruits, fruit juices, fruit salads, cheese, raw chicken and ground beef were collected from popular street markets in the cities of Guayaquil, Quito and Cuenca. Populations of total aerobic mesophilic bacteria (TAM), total coliforms (TC), fecal coliforms (FC), Escherichia coli (EC), Salmonella enterica and Listeria monocytogenes were examined on composited samples by plate count following the local regulations (Norma Tecnica Ecuatoriana - INEN) for each kind of food. The individual and interaction effects of the city and food type on the levels of each bacterial group was assessed by two-way ANOVA. Selected colonies from each culture were identified using Biolog OmniLog ID and sequencing of the V3-V4 region on the 16S rRNA gene. Average TAM, TC, FC and EC levels were 5.10 ± 0.12, 2.50 ± 0.16, 1.09 ± 0.12 and 0.83 ± 0.12 log CFU/g or mL, respectively, with significant variations among the cities. The prevalence of Salmonella in chicken and sauces as well as L. monocytogenes in cheese and fruit salad was greater than 20 %.  Opportunistic pathogens including Klebsiella pneumoniae, Staphylococcus sciuri, and Enterococcus spp. were frequently identified in the samples from all three cities. High prevalence of spoilage microorganisms such as Bacillus amyloliquefaciens and biocontrol bacteria such as Lactococcus lactis was also observed. This is the first report on the microbiological quality of food from Ecuador.