Plant-based dairy alternatives (PBDA) are products derived from plant sources, developed as substitutes for conventional dairy. The global market for PBDA and organic products has grown substantially, driven by perceptions that organic plant-based options are healthier and more sustainable. This study evaluated the nutritional profile of organic plant-based milk (PBMA) and yoghurt alternatives (PBYA) available in Portugal. Products were classified by primary plant-based ingredient and nutritional profile was assessed using the UK traffic light labelling system. Among PBMA (n = 97), median energy values ranged from 29 to 60 kcal/100 ml. Soy-based beverages had the highest protein content (3.3 g/100 ml), while coconut-based products exhibited the highest saturated fat content (up to 1.7 g/100 ml). Carbohydrates and sugars varied widely, with rice-based and mixed products showing the highest values (up to 11.0 g/100 ml and 5.5 g/100 ml, respectively). Only 4% of PBMA met favorable nutritional profile criteria, mainly due to excessive sugar content. For PBYA (n = 48), median energy content ranged from 75 to 115 kcal/100 g. Soy-based yoghurts had the highest protein content (3.8 g/100 g), whereas coconut-based alternatives showed the highest saturated fat levels (up to 6.8 g/100 g). Only 10% of PBYA met the nutritional adequacy criteria, with sugar content again being the primary limiting factor. Overall, despite organic certification, most products showed suboptimal nutritional profiles. These findings highlight the need to promote food and nutrition literacy, to support informed consumer choices, particularly through critical evaluation of nutrition labels and ingredient lists.