The nature of the complexing agents used in the bioscouring process of cotton fabrics aiming to eliminate the non-cellulosic compounds (pectin, waxes, etc.) and to improve the hydrophilic and wetting properties influences the thermal behaviour and the FT-IR spectra of the textile materials. In this paper, we study the influence of the experimental conditions and complexing agent nature (sodium citrate or disodium EDTA salt) on the pectin elimination in bioscouring treatment of cotton fabric by FT-IR and TG/DTG/DTA analysis. The changes from FT-IR spectra of the specific bands (absorbance intensity at 2916, 2852, 1732 and 1640/1642 cm−1) were evaluated. The thermal behaviour of the investigated samples’ fabric by using TG/DTG/DTA analysis was studied at 30–600 °C temperature range, in air atmosphere. All samples showed three mass-loss steps due to the elimination of humidity, decomposition of the non-cellulosic and cellulosic components (main degradation stage of the samples) and thermo-oxidative decomposition of the formed degradation products. The Tonset values corresponding to the main decomposition step, the mass-loss values (%Δm) and the % residual mass (at 600 °C) were influenced by the complexing agent nature as well as the concentration and the action time of the commercial enzyme product. In addition, the calcium content of some samples treated with and without ultrasound was determined using atomic absorption spectroscopy method (AAS) in order to correlate the results with TG/DTG/DTA analysis. The obtained results have shown that the synergistic action of experimental conditions (enzyme concentration, pH, enzyme product action time, ultrasound) and the presence of sodium citrate as a biodegradable complexing agent led to the elimination of a higher amount of pectin from the cotton samples than that eliminated when using EDTA.