HS-SPME-GC-FID and -MS were used to track the extent of lipid oxidation in shelled and inshell raw almonds, stored under different temperature/relative humidity conditions, over 24 months. In total, 5 aldehydes, 13 alcohols, 4 alkanes, and 10 miscellaneous organic volatiles were identified and quantified. The extraction temperature, extraction time, and desorption period of major almond volatiles were optimized. Quantitation was carried out in two ways: calibration curves of hexanol-d13 and hexanal-d13, relating peak area to concentration, were developed; and the standard addition method was performed using these isotopologic-deuterated standards and an ultrapycnometer to determine the density of ground almond powder (GAP). With both methods of quantitation yielding <15% differences in calculated μg/mL concentrations of volatiles, the employment of deuterated isotopologues of analytes-of-interest was validated. Relative quantitation of these volatiles indicated that storage parameters (i.e., temperature and % relative humidity) were influential in their development, especially for volatiles that were known secondary lipid oxidation products of linoleic acid. To illustrate, hexanal levels within the first 8 months of storage at 25 °C achieved levels of 5.7 and 7.3 μg/g GAP when stored under low- and high-humidity conditions, respectively. Hence, the comparison of volatile contents between inshell and shelled almonds throughout storage highlights a potential for the utilization of inshell storage as a means of promoting flavor stability, although this efficacy may be dependent on shell characteristics of the almond cultivar in question.