Green ‘Anjou’ pear and its bud mutation, red ‘Anjou’ were compared to understand their differences in phenolic metabolism and its effect on primary metabolism. In the flesh of the two cultivars, no difference was detected in the concentration of any phenolic compound, the transcript level of MYB10 or the transcript levels or activities of key enzymes involved in anthocyanin synthesis. Compared with green ‘Anjou’, the shaded peel of red ‘Anjou’ had higher anthocyanin concentrations, higher transcript levels of MYB10 and higher activity of UDP-glucose:flavonoid 3-O-glycosyltransferase (UFGT), suggesting that MYB10 regulates UFGT to control anthocyanin synthesis in red ‘Anjou’ peel. In the sun-exposed peel, activities of phenylalanine ammonia lyase, dihydroflavonol reductase, flavonol synthase and anthocyanidin synthase as well as UFGT were higher in red ‘Anjou’ than in green ‘Anjou’. The peel of red ‘Anjou’ had higher activities of sorbitol dehydrogenase, raffinose synthase and sucrose synthase and higher levels of raffinose, myo-inositol and starch, indicating that sorbitol metabolism, raffinose synthesis and starch synthesis were upregulated in red ‘Anjou’. The flesh of red ‘Anjou’ had higher concentrations of glucose, but lower activities of ATP-dependent phosphofructokinase, pyruvate kinase and glucose-6-phosphate dehydrogenase and lower dark respiration. The peel of red ‘Anjou’ had higher activities of glutaminase, asparagine synthetase and asparaginase, and higher concentrations of asparagine, aspartate, alanine, valine, threonine and isoleucine. The effects of anthocyanin synthesis on primary metabolism in fruit peel are discussed.