Innate immunity plays a determinant role in high fat diet (HFD)-induced insulin resistance. This study compares the effects of immunonutritional bioactives from Chenopodium quinoa (WQ) or Salvia hispanica L. (Ch) when used to partially replace wheat flour (WB) into bread formulations. These flours were chosen to condition starch and lipid content in the products as well as because their immunonutritional activity. To be administered with different bread formulations, HFD-fed C57BL/6J mice were distributed in different groups: (i) wild type, (ii) displaying inherited disturbances in glucose homeostasis, and (iii) displaying dietary iron-mediated impairment of the innate immune TLR4/TRAM/TRIF pathway. We analyze the effects of the products on glycaemia and insulin resistance (HOMA-IR), plasmatic triglycerides, intestinal and hepatic gene expression and variations of myeloid (MY), and lymphoid (LY) cells population in peripheral blood. Our results show that feeding animals with WQ and Ch formulations influenced the expression of lipogenic and coronary risk markers, thus attaining a better control of hepatic lipid accumulation. WQ and Ch products also improved glucose homeostasis compared to WB, normalizing the HOMA-IR in animals with an altered glucose and lipid metabolism. These positive effects were associated with positive variations in the peripheral myeloid cells population.