Consumption of ultra-processed food (PF) is associated with obesity risk compared with whole food (WF) intake. Less is known regarding the intake of gluten-free (GF) food products. The purpose of this study was to directly compare the thermic effect (TEM), substrate utilization, hunger/taste ratings, and glucose response of three different meals containing PF, WF, and GF food products in young healthy women. Eleven volunteers completed all three iso-caloric/macronutrient test meals in a single-blind, randomized crossover design: (1) whole food meal (WF); (2) processed food meal (PF); or (3) gluten-free meal (GF). TEM was significantly lower following GF compared with WF (−20.94 kcal/meal, [95% CI, −35.92 to −5.96], p = 0.008) and PF (mean difference: −14.94 kcal/meal, [95% CI, −29.92 to 0.04], p = 0.04), respectively. WF consumption resulted in significantly higher feelings of fullness compared to GF (mean difference: +14.36%, [95% CI, 3.41 to 25.32%], p = 0.011) and PF (mean difference: +16.81%, [95% CI, 5.62 to 28.01%], p = 0.004), respectively, and enhanced palatability (taste of meal) compared to PF meal (mean Δ: +27.41%, [95% CI, 5.53 to 49.30%], p = 0.048). No differences existed for substrate utilization and blood glucose response among trials. Consumption of a GF meal lowers postprandial thermogenesis compared to WF and PF meals and fullness ratings compared to a WF meal which may impact weight control and obesity risk over the long-term.