Cellular mechanisms underpinning the hard-to-cook phenomenon are poorly understood. Navy beans (Phaseolus vulgaris) from the same cultivar but grown in different regions of North America showed different canning characteristics. Up to 46.4% more force was required to disrupt hard beans (HB) grown in Ontario compared with soft beans (SB) grown in Manitoba. HB absorbed 12.5% and 14.7% less water during blanching and canning, respectively. Microscopic assessment revealed that canning led to swelling of middle lamella and cell walls, but preservation of cell adhesion in both types of beans. Immunofluorescence microscopy showed reduced labelling of methyl-esterified homogalacturonan (HG) and more non-methyl-esterified HG and arabinan epitopes in HB. Compositional analysis indicated that the polysaccharides from HB were less water soluble and enriched in neutral sugars, including 46.5% more arabinose and 51.8% more galactose than in SB. ELISA analysis of polymers in the canning medium supported the increased solubility of cell wall polymers in SB. In the same cultivar, growth region affects cell wall properties with consequences for processing, eating and nutritional quality.