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(1) Background: Multiple attempts have been conducted to correlate milk keeping quality with chemical, physical or bacteriological parameters. These methods only measure the chemical changes in milk produced by bacteria. Headspace solid-phase micro-extraction (HS-SPME) is an economic and recent method used to measure both volatile compounds and microbial load in milk, also allowing to keep the quality of the milk product. (2) Methods: The present study was conducted to identify and measure the off-flavoring volatile compounds through gas chromatography coupled with flame ionization detector (GC-FID) and the microbial load of pasteurized fluid milk stored at different temperatures, as a possible indicator of its keeping quality. (3) Results: The highest results were obtained to acetone, followed by butanone, pentanal and ethanol. These mean values were significantly enhanced from the 0 to 19th day of storage, at 10 °C. At day 19th, the minimum score for aroma, flavor and overall acceptability were also recorded as 4.33 ± 0.17, 4.02 ± 0.06, 4.00 ± 0.04, respectively. Likewise, maximum values for standard plate count (Log10 CFU 15.54 ± 0.40 mL−1) and total psychotroph count (Log10 CFU 11.67 ± 0.30mL−1) were reported at 10 °C and 4 °C. (4) Conclusion: HS-SPME/GC-FID methodology revealed to be very sensitive and capable to be applied in volatile compounds quantification in pasteurized milk produced during the storage period at different temperatures.