The tomato processing industry generates a significant amount of a by‐product (pomace), which is a mixture of peels and seeds. The purpose of this study was to compare the effects of conventional oven‐roasting (at 120°C, 150°C, and 180°C for 25 min) and innovative microwave‐roasting (at 240, 388, and 536 W for 3 min) pretreatments on the physicochemical properties, fatty acid profiles, bioactive contents, and aroma profiles of tomato seeds and their hexane‐extracted oils. The total flavonoids contents (TFCs) of the seeds decreased from 258.40 to 141.20 mg quercetin equivalent (QE) per kg after roasting. All roasting treatments improved the extractability of both α‐ and γ‐tocopherols. The amounts of total tocopherols in the seeds increased from 917.61 to 1256.25 mg kg–1 after pretreatment. Luteolin was found to be the most abundant phenolic in seed oils, increasing from 10.68 to 91.72 mg kg–1, followed by quercetin, ferulic acid, and catechin. Within each roasting technique, the ones treated at 150°C and 338 W yielded the oils with the highest concentrations of aroma compounds, 418 and 92 mg kg–1, respectively. The detrimental effect of microwave‐roasting on these compounds was more pronounced. In conclusion, microwave‐roasting at shorter times than conventional roasting produced tomato seed oils with well‐preserved bioactive components and few unfavorable changes.