Dough-derived cell wall fragments isolated by ultracentrifugation were largely derived from the starchy endosperm, with some fragments deriving from the aleurone and outer layers, as indicated by fluorescence microscopy. Dough mixing had little effect on the structure and composition of cell wall fragments compared to thin grain sections, as determined by Fourier transform infrared (FTIR) and (1)H nuclear magnetic resonance (NMR) spectroscopy. These analyses confirmed that the fragments largely comprised water-unextractable arabinoxylan and β-glucan. FTIR microspectroscopy of dough-derived cell wall fragments prepared from five bread wheat cultivars showed that two largely comprised highly substituted arabinoxylan (cv. Manital and San Pastore), one comprised a mixture of low, medium, and highly substituted arabinoxylan (cv. Hereward), and the remaining two comprised a greater proportion of low substituted arabinoxylan (cv. Claire and Yumai 34). Yumai 34 yielded a greater mass of cell wall material, and its cell walls comprised a high proportion of medium substituted arabinoxylan. Such methods will allow for the impact of bakery ingredients and processing on endosperm cells, including the addition of xylanases, to be investigated in the future to ensure any potential health benefits arising from wheat breeding are realized in the food that reaches the consumer.