Cell wall (CW) degradation causes texture loss of plant-based products after processing. However, these losses differ in intensity, which could be due to cell wall structure or plant tissue internal pH conditions. To distinguish these two factors, CWs isolated from apple, beet and kiwifruit were subjected to boiling at pH 2.0, 3.5 and 6.0. Pectin depolymerization was the least pronounced at pH 3.5, while galacturonic acid contents of all CWs decreased at pH 6.0 due to the β-elimination. Pectins were solubilized, and their size decreased with increased pH during CW treatment. At pH 6.0, degrees of methylation decreased mostly in apple and beet CWs while galactose decreased more in kiwifruit CW. At pH 2.0, arabinan was lost in apple and beet CW due to acid hydrolysis. Apple CW was the most susceptible to degradation either at pH 2.0 or 6.0, while beet CW was more degraded at pH 2.0. In contrast, kiwifruit CW was the least susceptible to degradation whichever the pH. Acid hydrolysis and β-elimination appeared to be common mechanisms that cause loss of neutral sugars, often from pectin side chains, and galacturonic acid, respectively, but their effects were of different intensities. This work has a guiding significance for improving texture in the thermally canning process.