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White wheat flour contains a range of polar metabolites, including amino acids, organic acids, sugars (mono-, di- and tri-saccharides) and methyl donors (choline and betaine), which may contribute to a healthy diet. We have used 1H NMR to quantify the concentrations of 28 polar metabolites in the white flour of a double haploid population of the cross Malacca x Hereward comprised of 106 lines grown in field trials in 2020 and 2021 and a sub-set of 76 lines grown in 2005. This identified a total of 106 QTL for individual or groups of metabolites of which three were present in two of the three datasets. These “stable” QTLs include two for betaine, QBet-4D.1 and QBet-5B.1, explaining 14-31% and 21-24% of the variation, respectively, and one for succinate, QScc-7B.1, explaining 16-18% of the variation, with average additive effects of + 0.09(M), +0.03(M), and +0.06 (H) mg. g-1 of flour. Betaine has established health benefits in humans by remethylating homocysteine, which is a risk factor for cardiovascular disease. The availability of markers from our study will therefore allow the selection of new types of wheat with higher betaine in white flour.