Wastewater treatment plants (WWTPs) are one of the most energy-intensive industries. Every stage of wastewater treatment consumes energy, which is the primary contributor to WWTP costs. Adsorbents and process optimization are critical for energy savings. The removal of dyes from industrial wastewater by adsorption using commercially available adsorbents is inefficient. Metal−organic frameworks (MOFs) have outstanding properties that can improve separation performance over current commercial adsorbents, and thus, these materials represent a milestone in improving dye removal in water treatment methods. In this work, three types of metal−organic frameworks (Fe-BTC, Cu-BTC, and ZIF-8) have been investigated as prospective adsorbents for methyl orange removal from water in batch setups. The results showed that at 15 mg/L MO initial concentration and 100 mg dosage, Fe-BTC had the highest removal efficiency of 91%, followed by ZIF-8 (63%), and finally Cu-BTC (35%), which exhibited structural damage due to its instability in water. Fe-BTC maintained consistent adsorption capacity over a wide range of pH values. Furthermore, a 23 full factorial design analysis was implemented to evaluate the conditions for maximum MO-removal efficiency. The main effects, interaction effects, analysis of variance (ANOVA), and the Pareto chart were reported. The statistical analysis demonstrated that the MOF type was the most significant factor, followed by dosage and initial concentration. The analysis indicated that the type of MOF and dosage had a positive effect on the removal efficiency, while the initial concentration had a negative effect. The two-way and three-way interactions were also found to be significant.