To reduce the negative impact on the environment, architects, designers, and construction companies need to find and apply eco-friendly and sustainable building solutions. Due to its renewable nature and numerous advantages, timber has become an attractive substitute for steel and concrete in both residential and non-residential construction projects. However, timber application in the construction of grocery stores is a relatively new concept. The purpose of this research is to propose three alternative timber-based structural systems for a grocery store in Lithuania and to select the most efficient option based on multi-criteria decision-making methods. Three alternative glued laminated timber (glulam) structural systems—the glulam column and truss system, the glulam three-hinge frame system, and the glulam column and double-tapered beam system—were designed. The systems were evaluated against ten criteria, reflecting structural properties, cost efficiency, assembling complexity, and aesthetics. Multiple-criteria assessments by the COmplex PRoportional ASsessment (COPRAS) method and simple additive weighting (SAW) method revealed that the best-performing alternative is the glulam column and double-tapered beam system due to the lower cost of load-bearing structures, the smaller quantity of required steel details and fittings, and the highest maximum utility ratio according to serviceability limit states compared to other alternatives.