Coffee cold brews have been gaining prominence and popularity among consumers worldwide. However, only a few studies have systematically analyzed their chemical composition or evaluated microbiological safety aspects. This study aimed to evaluate the survival of Bacillus cereus and Escherichia coli in cold brews prepared from roasted and ground Coffea arabica and C. canephora seeds using the following preparation methods: immersion without filter (INF), immersion in a cotton filter bag (ICF), vacuum (Vac.) and cold dripping (Drip.). Traditional hot dripping methods using filter paper (HDFP) and cotton filter (HDCF) were also tested for comparison. Water at 4 °C or 25 °C was intentionally contaminated (105 CFU/mL) with cells of Escherichia coli ATCC 25922 (EC) and Bacillus cereus F4433 (BC) before coffee extraction and refrigeration at 4 °C. Coffee concentrations of 5, 10, and 15% were tested. Analyses of pH, soluble solids, nine chlorogenic acids and two lactones (CGA), caffeine, trigonelline, and melanoidins were performed. Results were compared by ANOVA, followed by the Fisher’s test, Pearson correlation, Variable Importance in Projection (VIP), and Cluster analyses, with a significance level of 5%. EC and BC were not detected (<10 CFU/mL and < 1 CFU/mL, respectively) after preparing C. arabica and C. canephora hot brews. In cold brews, the higher the extraction of soluble solids and bioactive compounds (with the highest occurring at 25 °C), the lower the counts of inoculated microorganisms during 24 h of storage. BC was not detected after 24 h of extraction and/or storage in the drinks obtained by ICF and Drip. at 5%, 10%, and 15% and INF and Vac. at 15%. EC was not detected in ICF and Drip. at 10 and 15%, and in INF at 15%. C. canephora brews exhibited higher levels of soluble solids, CGA, caffeine, and melanoidins than C. arabica brews. Based on these results, it can be concluded that in the absence of thermal processing as in hot brews, more concentrated cold brews, such as 15%, produced at 25 °C by dripping and immersion methods, are preferable for later dilution due to the higher content of soluble solids and bioactive compounds that contribute reducing the number of microorganisms in the beverage.