The food industry is increasingly concerned with operational sustainability and food waste reduction. In the United States, the tomato industry was worth $1 billion in 2020, and tomatoes are currently ranked second as the most consumed vegetable after potatoes. Tomato processors have striven to valorize pomace by-products, which contain seeds with valuable compounds such as 45% fiber, 30% oil, and 26% protein. The U.S. peach industry, which was worth $599 million in 2017, is also looking for alternative ways to utilize their seeds, made up of 52% oil. Both tomato and peach seeds are rich in bioactive compounds such as carotenoids and polyphenols, respectively. Meanwhile, global edible oil production is forecasted to reach 632 million tons in 2022, and there is increasing interest to produce specialty oils. Organic solvent extractions are commonly used to extract oils from various commodities in the food industry, but this method comes with some environmental concerns, such as toxicity and flammability. Enzyme-assisted aqueous extractions (EAEP) have been proposed as a green alternative to solvent extractions of oilseeds. However, research on the economic feasibility of this process has been limited. There is a need for a better understanding of the potential of EAEP and performing such analysis on peach and tomato seeds would be valuable based on the importance of these commodities in California and in the U.S. in general. To determine whether applying such a process to tomato and peach seeds would be valuable, data on oil yields from EAEP, quality of the extracted oils, and economics associated with EAEP is needed. The U.S. snack food industry was worth approximately $42 billion as of 2019, and this market continues to grow as an increasing number of people eat snacks as meal replacements. There is also growing consumer demand for natural and functional foods, which offer health benefits beyond basic nutritional value, such as reducing risk of disease. Therefore, this consumer landscape provides excellent opportunities for by-products from vegetable and fruit processing to be transformed into functional ingredients. With these key ideas in mind, the objectives of this research were 1) to determine the impact of various extraction factors on oil yields from EAEP of tomato and peach seeds; 2) to evaluate the effect of aqueous extractions on oil quality; 3) study whether these processing steps are economically feasible for industrial commercialization and 4) identify another potential use for tomato pomace as a functional ingredient in snack food application. Tomato and peach seeds were each isolated and ground into a flour, then analyzed for fiber, fat, protein, moisture, and ash content. The effects of pH (set to 3, 9, and sequential adjustment of 3 followed by 9), time (2–8 h), and addition of cellulase, protease, and 1:1 enzymatic cocktail at a concentration of 4% were evaluated during aqueous extractions of tomato oils. Peach oil extractions were evaluated for the same parameters except for time which was fixed at 2 h. The impact of the pH of aqueous extractions on the oxidative stability and nutritional composition of tomato and peach oils were also determined. Techno-economic analyses were conducted using Superpro software to estimate operational costs and profits from this process. To assess the value of tomato by-product as a functional ingredient, pomace flour was added to crisp snacks at usage levels of 0 and 7% (w/w flour basis). Crisp snacks were stored at ambient room temperature and frozen temperatures (-23 °C) for ten weeks. Proximate analyses on the crisp snacks were conducted. Sensory evaluation was performed over time using hedonic scoring surveys. For tomato seeds, the highest oil yield (41%) was obtained during 2 h extractions at pH 9, which were 68% higher than from 2 h extractions performed at pH 3. Enzyme addition was only beneficial during 8 h extractions of tomato seeds using 4% cellulase at pH 3, which led to 53% higher oil yield compared to the control performed in the same conditions without enzymes. Increasing incubation time from 2 to 8 h improved oil yields by 63% for cellulase extractions at pH 3 and 69% for protease extractions at pH 9. Peach oil yield of the controls at pH 9 (53%) and the yield obtained with protease extractions at pH 9 (45%) were approximately eight times higher than all extractions set to pH 3. Once extracted, some properties of the tomato and peach oils were determined. The pH of the aqueous extractions did not have a significant effect on quality parameters on both tomato and peach oils, except for polyphenol content, DPPH production, peroxide and TBARS values. Overall, both tomato and peach oils had peroxide and free fatty acid values comparable to other specialty oils, such as sunflower and sesame oils. From a techno-economic point of view, tomato oil production at flow rate of 1,752,000 kg pomace/yr garnered $13 million in profit (equivalent to $7.42/kg pomace) after a payback time of 1.6 years, which was more profitable than the industry’s current pomace disposal practice. Peach oil processing became profitable once the production scale reached 65,700,000 kg pits/yr, which led to $15.5 million in profit ($0.24/kg pits). Overall, production of tomato oil was more profitable than peach oil. When tomato pomace was added into crisp snacks at 7% concentration, fiber increased by 35.2% compared to the control. Moisture content and water activity for the control and pomace crisp snacks remained constant during room temperature and frozen storage for ten weeks. However, the addition of tomato pomace led to a bitter aftertaste of the crisp snacks and reduced overall liking scores by panelists compared to scores for the control crisp snacks. Overall, this research took multiple, innovative approaches to valorize tomato and peach seeds, while also studying the economic, environmental, and industrial implications of such approaches. It highlighted alternative, sustainable strategies of how tomato and peach by-products could be repurposed to reduce waste and make value-added food products.