Understanding the microstructural evolution of the cake layer during ultra-filtration is essential for optimizing operating conditions and developing effective cleaning strategies in wastewater treatment systems. This study investigates the effect of variations in the carbohydrate-to-protein-to-mineral ratio on the structural properties of biofouling that forms on the membrane surface under controlled laboratory conditions. A synthetic wastewater matrix was formulated using low-molecular-weight chitosan (LWC) and bovine serum albumin (BSA), with C/P ratios of 0.25, 0.42, 0.75, 1.49, and 1.85. The mineral content was adjusted using NaCl, NaHCO3, and three concentrations of CaCl2, resulting in 20 different solution scenarios. Ultrafiltration tests were conducted under constant pressure, with real-time monitoring of porosity, fractal dimension, and flow loss. Results revealed a progression of fouling mechanisms, transitioning from standard pore blockage to cake-layer dominated regimes. The fractal dimension values (2.85–2.96) indicated the development of highly complex three-dimensional structures. Biopolymer–mineral interactions were shown to influence the morphology and density of the fouling layer significantly. These findings provide a framework for optimizing filterability conditions and enhancing the performance of full-scale membrane bio-reactor (MBR) systems.