Acrylamide (AA), a molecule which potentially increases the risk of developing cancer, is easily formed in food rich in carbohydrates, such as biscuits, wafers, and breakfast cereals, at temperatures above 120 °C. Thus, the need to detect and quantify the AA content in processed foodstuffs is eminent, in order to delineate the limits and mitigation strategies. This work reports the development and validation of a high-resolution mass spectrometry-based methodology for identification and quantification of AA in specific food matrices of biscuits, by using LC-MS with electrospray ionization and Orbitrap as the mass analyser. The developed analytical method showed good repeatability (RSDr 11.1%) and 3.55 and 11.8 μg kg−1 as limit of detection (LOD) and limit of quantification (LOQ), respectively. The choice of multiplexed targeted-SIM mode (t-SIM) for AA and AA-d3 isolated ions provided enhanced detection sensitivity, as demonstrated in this work. Statistical processing of data was performed in order to compare the AA levels with several production parameters, such as time/cooking temperature, placement on the cooking conveyor belt, color, and moisture for different biscuits. The composition of the raw materials was statistically the most correlated factor with the AA content when all samples are considered. The statistical treatment presented herein enables an important prediction of factors influencing AA formation in biscuits contributing to putting in place effective mitigation strategies.