The concentration of 2-heptanone, derived from decarboxylation of β-ketoacids naturally present in milk, has been shown to be affected by the severity of heat-treatment applied to cows' milk. In this paper, the influence of microfiltration (MF) coupled with mild pasteurisation, on the development of this compound in goats' milk was investigated. Moreover, the effect of these treatments on the microbial content was evaluated. Solid phase microextraction coupled with GC-MS system, was used to determine the 2-heptanone content of samples at different process steps: raw skimmed milk (before and after MF), cream (before and after pasteurisation), reconstituted whole milk (before and after pasteurisation). To obtain an absolute concentration of 2-heptanone, specific calibration curves for the different matrices were developed. Results demonstrated that the MF process did not increase the 2-heptanone concentration. The values found for reconstituted whole goats' milk were mainly due to the heat treatment applied to cream; nevertheless, they were within the range observed for milk only subjected to the pasteurisation treatment. MF improved the microbiological quality resulting in an extended shelf-life.