Gel-based food systems, including plant-based and animal-derived formulations, are increasingly recognized as structure-driven platforms for controlling quality, safety, and functional stability. The growing demand for plant based foods has intensified the need to design gel networks capable of matching or exceeding the performance of conventional protein systems. A structure–function–safety framework is introduced to describe how processing conditions and network architecture regulate water mobility, mass transfer, oxidative stability, and microbial susceptibility. Gelation mechanisms in plant proteins (e.g., soy, pea, wheat gluten), myofibrillar proteins, gelatin, and protein–polysaccharide composites are discussed in relation to microstructure and rheological behavior. The influence of processing variables, including thermal history, ionic conditions, pH, and non-thermal technologies (e.g., high-pressure processing, ultrasound, pulsed electric fields), is evaluated for their ability to tailor network structure and performance. Beyond conventional quality attributes, gel systems function as active matrices that control oxygen diffusion, modulate antimicrobial and antioxidant release, and influence microbial growth. This integrated perspective supports a design-oriented approach to food systems, enabling predictive control of functionality and safety, while highlighting current challenges and future directions in characterization, modeling, and material design.