The aim of this study was to evaluate the effect of extruded preparations on the bioactive and nutritional properties, vitamin B content, volatile compound profile, and quality of whole wheat bread. Extruded preparations based on stale bread (secondary raw materials) and apple pomace (byproducts) were used as bread additives. It was found that the preparations did not enrich the bread in protein but in health-promoting compounds, especially gallic acid, protocatechuic acid, caffeic acid, p-coumaric acid, rutin, quercetin, and B vitamins. Extruded preparations had a positive effect on the quality of the bread produced, such as yield and cohesiveness, and gave it a pleasant aroma. It was shown that among all the examined bread samples with added extruded preparations of stale bread, the cornmeal and apple pomace bread samples with 15% extruded preparation (containing 55% cornmeal, 30% stale bread, and 15% apple pomace) had sufficient nutritional value, the highest amounts of gallic acid, protocatechuic acid, p-coumaric acid, caffeic acid, rutin, and quercetin; medium amounts of ellagic acid; high antioxidant activity determined in vitro using four methods (by DPPH, ABTS, power (FRAP), and Fe(II) chelating assays); adequate quality; and significant amounts of vitamins, especially B1, B2, and B3. This type of extruded preparation should utilize apple pomace, which is a byproduct, and stale bread, which is a secondary waste. Such a combination is an excellent low-cost, easy, and prospective solution for the baking industry that could be applied to obtain bread with elevated nutritional value and enhanced health potential, as proven in this publication.