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Health-protective functional foods are gaining popularity in the world of nutrition because they promote excellent health while decreasing pharmaceutical burdens. Chia seeds (CS) (<i>Salvia hispanica</i> L.), the greatest vegetative source of α-linolenic acid, bioactive proteins, and fibers, are among the top unconventional oilseeds shown to have bounteous benefits against various non-communicable diseases. Purposely, this study was designed to integrate roasted CS powder into white-flour-based ordinary bakery goods to improve their nutritional and nutraceutical profiles. CS efficacy in normal and hyperlipidemic Sprague-Dawley rats resulted in mitigating blood glucose, triglycerides, total cholesterol, and low-density lipoprotein cholesterol while elevating high-density lipoprotein cholesterol, hematocrit, hemoglobin, red blood cell counts, and platelets. The nutritional profiling of chia-fortified muffins indicated significant increases of 47% in fat, 92% in fiber, 15% in protein, and 62% in minerals. The farinographic experiments of CS-blends revealed generally improved dough quality features with a significant rise in the degree of softening as fortification levels increased. A marketable recipe for CSF-muffins with several degrees of fortification demonstrated a significant rise in fat, 92% rise in fiber, 15% rise in protein, and 62% rise in minerals. Sensorial evaluation by trained taste panelists revealed a maximum appraisal of the 15% chia-fortified muffins due to aroma, appearance, and overall acceptability, and were forwarded for being acceptable for commercialization.