Fruits and fruit pulps are widely consumed worldwide due to their nutrients, flavors and varieties. However, these products become contaminated with pathogens during harvest or production, which are risks to consumers. This study analyzed the microbiological quality of frozen fruit pulps and minimally processed fruits sold in supermarkets and the presence Salmonella sp. and pathogenic Escherichia coli. Almost all frozen fruit pulps samples were adequate to consume, only one samples of unpasteurized mango pulp was positive for E. coli carrier of est1b gene that codify thermostable toxin of Enterotoxigenic E. coli. Minimally processed fruits presented high yeast and mold counts in 36.25% (29/80) of the samples and 27.6% (22/80) had thermotolerant coliforms. In addition, one sample of grated coconut had E. coli and one sample of melon honeydew had Salmonella sp. E. coli O157:H7 was absent in all samples of minimally processed fruits. E. coli showed greater resistance to ampicillin and chloramphenicol. Multidrug resistance was observed in 14.3% (2/14) of E. coli isolates. Only one strain of Salmonella sp. was resistant to antibiotic sulfamethoxazole/trimethoprim. Therefore, the enforcement of pasteurization in the fruit pulp processing, as well hygienic-sanitary control in lead up of minimally-processed fruits and temperature control in storage are recommended to minimize the risk of foodborne disease.