Aerogel sponges of bio-based polymers loaded with metal–organic frameworks (MOFs) are highly promising for environmental applications, but a central challenge is to improve their stability and efficiency for removal processes. Here, the effective incorporation of the MOFs MIL-100(Fe) and ZIF-8 in composite aerogels of chitosan–pectin–lactic acid is reported. The presence of pectin was critical to loading the MOFs efficiently and homogeneously, while the incorporation of lactic acid induced a large increase in the Young’s modulus and provided structural preservation in aqueous solutions. The presence of MOFs enhanced the removal of two dyes, methyl orange (MO) and methylene blue (MB), under batch and flow conditions, with removal efficiencies of methyl orange of about 85% and 90% when loaded with ZIF-8 and MIL-100(Fe), respectively. Bentonite, celite 545, and two ionenes were loaded for comparison. Factors beyond charge-to-charge electrostatic interactions influenced the removal, since no correlations were obtained between the electrical charges of dyes, fillers, and polymers. The kinetic data were analyzed by adapting the Langmuir kinetic model, incorporating absorption and desorption processes, which allowed the recovery of the respective rate constants.