Paçoca is a typical Brazilian confectionery of Indigenous origin prepared by mixing ground roasted peanuts, sugar, and salt. A total of 52 samples of paçoca (37 pressed, 15 cooked), produced and sold in the state of São Paulo, were evaluated for aflatoxin content (AFB1, AFB2, AFG1 and AFG2), moisture content and water activity. The microbiological quality was assessed by counting mesophilic aerobic bacteria, fungal and yeast counts, most likely number of thermotolerant coliforms and Escherichia coli and Salmonella sp. The limit of quantification (LOQ) by Ultra Performance Liquid Chromatography coupled to the Mass Spectrometer (UPLC-MS/MS) ranged from 0.29 μg kg−1 for AFB1 and AFG2; 0.36 μg kg−1 for AFG1 and 0.37 μg kg−1 for AFB2. The recovery averages were 89.2, 83.5, 80.5 and 82.8% for AFB1, AFB2, AFG1 and AFG2. 71% of the samples showed aflatoxin contamination, ranging from 0.29 to 38.8 μg kg−1 (mean of 7.06 μg kg−1). Six samples (16%) exceeded the limit value tolerated by the Brazilian guideline for AFT (20 μg kg−1). The mean AFT content in cooked paçocas (19.55 μg kg−1) was higher than the levels in pressed paçocas (9.08 μg kg−1) (p < 0.05). AFB1 had a higher incidence in the two groups of paçocas (75% pressed and 60% cooked). The mean moisture content and water activity of cooked paçocas (8.86% and 0.7081) were higher than those of pressed paçocas (2.08% and 0.4863). Twenty-one samples (56%) showed fungal and yeast contamination ranging from 1.0 to 4.25 log CFU g−1. The total count of aerobic mesophilic bacteria in cooked paçocas (4.85 log CFU g−1) was also higher than in pressed paçocas (2.77 log CFU g−1) (p < 0.05). E. coli was confirmed in these samples in the range of 3.0–160 NMP g−1. Salmonella sp. was detected in 2 samples of pressed paçocas, indicating poor hygiene, inefficient heat treatment or possible cross-contamination. The results of this study demonstrate the need for greater control of the paçoca production chain through the adoption of Good Manufacturing Practices and process control, to prevent exposure of the population to aflatoxins and possible pathogenic microorganisms.