Non-communicable diseases are particularly prevalent among low-income individuals and are associated with the consumption of processed foods, fat, and sugars. This work aims to evaluate the impacts of a nutrition education intervention for low socio-economic individuals on sensory perception, health-related parameters and gut microbiota. Twenty low-income adults underwent a 4-week intervention. Dietary information (three 24 h recalls), detection thresholds and discrimination scores (salty and sweet), and severity of depressive symptoms (Beck Depression Inventory-II (BDI-II)) were collected. Fecal microbial composition and short chain fatty acids were determined by 16S ribosomal RNA-gene sequencing and gas chromatography, respectively. After the intervention, 35% of subjects presented higher compliance with dietary recommendations, increased consumption of vegetables and lignans and reduced consumption of processed meats and nitrosamines, together with depleted levels of Actinomycetota. Higher discrimination for salty and sweet and lower BDI-II scores were also obtained. This nutrition education intervention entailed changes in dietary intake towards healthier food options, reduced potentially carcinogenic compounds and improved scores for discrimination and severity of depressive symptoms. The confirmation of these results in future studies would enable the design of strategic policies contributing to the optimal nutrition of materially deprived families through affordable healthy plant-based interventions.