Off-odors produced by volatile compounds remain a major barrier to consumer acceptance of plant-based proteins. This study presents a novel two-stage fermentation strategy to effectively reduce undesirable volatiles in eight plant proteins. A sequential fermentation process was developed using Lactobacillus plantarum in Stage 1 and a traditional yogurt culture, Streptococcus thermophilus, Lactobacillus delbrueckii subsp. Bulgaricus and Lactobacillus acidophilus, in Stage 2. This method was applied to solutions of 9% soy, pea, chickpea, mung bean, faba bean, rice, barley-rice, and hemp proteins. Volatile profiles were analyzed via Selected Ion Flow Tube Mass Spectrometry (SIFT-MS) and sensory evaluation before and after fermentation. The two-stage fermentation resulted in significant deodorization, with 95–99% reduction in key odorants such as hexanal, 2-pentylfuran, methoxypyrazines, and sulfur compounds across all proteins. The sequential approach significantly outperformed a one-stage fermentation. Allulose enhanced L. plantarum activity while strawberry preserves supported traditional yogurt culture performance. Non-fermentable additives such as pectin, xanthan gum, and oil had minimal effects on volatiles. The proposed fermentation method offers an effective, scalable, and clean-label solution for mitigating off-odors in plant-based proteins. By leveraging microbial metabolism and formulation synergies, this strategy provides a foundation for developing more palatable plant-based dairy alternatives.