The aim of this study was to compare composites of pectin and carbon nanotubes (CNTs) prepared by chemical interaction (CI) or physical mixing (PM). CI-pectin-CNTs composite was produced by dispersing pectin and CNTs powder in ethanol, followed by refluxing at 60 °C. Biodegradable films of the pectin-CNTs composites were then produced and their mechanical, physicochemical and thermal properties were compared using rheological, tensile, oxygen permeation, integration, swelling and color tests. The CI-pectin-CNT films were more resistant to force, had greater stiffness and elongation at break and their water barrier properties were significantly greater than those of PM-pectin-CNTs. CI-pectin-CNTs films were lighter in color and showed greater integrity and swelling ratios. These confirmed substantial improvement of properties of pectin-CNTs films by chemical bonding as compared to physical mixing. Moreover, by chemical bonding the required level and hence the potential health risks of CNTs in biopolymer films and mixtures may be reduced.