Dye invasion in wastewaters is undeniably one of the crucial environmental concerns in addition to the supplement of toxic synthetic chemical flocculants used for color removal using the conventional coagulation-flocculation process. With the aim to improve the flocculation stage in terms of reagents safety and ensure dyes removal, the present study explores the flocculating effectiveness of two natural, stable, and eco-friendly cactus formulations, namely 60 °C oven-dried (DP) and lyophilized (LP) cladodes. Both formulations were assessed to treat cationic (Methylene blue; MB) and anionic (Methyl Orange; MO) dye solutions as a substitution attempt for the currently questioned employed synthetic chemical flocculants. Obtained results demonstrate that, in conjunction with alum as coagulant, the lyophilized powder (LP) bio-based flocculant appears to be the most efficient cactus formulation, showing a significant color (83%) and a turbidity (69%) abatement for the cationic dye (MB) and, respectively, 63% and 62% for the anionic one (MO). Additionally, the flocculation activity of the LP formula remained high over an eight-month period of storage. Moreover, based on the Fourier transform infrared (FTIR) spectroscopic analysis and the chemical characterization of cactus formulations, the occurring flocculation mechanisms of the dye removal are presumed to be based on both adsorption and bridging phenomena. Further, the significant color and turbidity decline achieved upon the addition of the lyophilized cactus cladodes powder (LP), enhancing thus the coagulation performance of the alum-based coagulant, proved the effectiveness of this bio-flocculant compared to the commonly used chemical flocculant (polyacrylamide). Hence, it was suggested that lyophilized cactus cladodes as a natural flocculant could be one of the effective surrogates to chemical flocculants conventionally used in wastewater treatment for the sake of a safer and sustainable environment.