To improve gluten-free (GF) muffin quality the pecan nut expeller (PNE) has been incorporated at two levels (20 and 30 g/100 g, P20 and P30, respectively) as a partial replacement for traditional flour mix, while water was adjusted to obtain iso-viscous batters than the GF-control. Process yield, aw, texture, color, crumb structure, and moisture were analyzed. PNE inclusion improved water-binding properties and let to obtain softer crumbs with more pores. Texture, crumb moisture, thermic transitions, fatty acid profile, and antioxidant capacity were studied during their storage. Product hardness increased over storage time but in a lower proportion for PNE-muffins, while chewiness increased for control and remained stable for them (2.43 N). Besides, starch retrogradation enthalpy diminished through the storage when the expeller was included. Higher antioxidant capacities were obtained in PNE-muffins, which were slightly lower by the storage time. Muffin's fatty acid profiles were almost stable during their storage in agreement with TBARS value that showed slight differences with time. Also, PNE-muffins presented higher PUFA contents (18.13 and 20.9 g/100 g for P20 and P30, respectively) with respect to the control. These results reflected that pecan nut expeller could be successfully incorporated into a GF- muffin with improvements in their physicochemical characteristics, PUFA content, antioxidant activity, and storage stability.