Mesoscopic structure of pectin with different molecular characteristics was investigated by means of small angle X-ray scattering (SAXS), electrokinetic measurements and data modelling. The influence of a broad range of pH (2–7) on chain conformation in the dilute and semi-diluted regime was investigated. Scattering data and concomitant analysis revealed two length scales at all environmental conditions studied. pH showed greater influence at acidic values (pH 2.0) enhancing the globular component of the structure due to association of galacturonic acid residues. Double logarithmic scattering intensity plots revealed fractal dimensions of 1.9 ± 0.2 in the low-q regime and 1.5 ± 0.2 in the high q-region, irrespectively of the specific environment. Increase in branching of RG-I regions of the polysaccharide chains enhanced the compact conformation irrespectively of the pH or concentration. The present work shows that radical changes in pectin conformation can be induced only under strongly acidic conditions a finding that has important consequences in tailoring the technological performance of these biopolymers.