Modern consumers turn to foods marketed as ‘natural/organic’ in their pursuit of healthier options. However, research that links such claims made on pack with improved nutritional composition is limited. The current analysis used data from all packaged foods available in the Hellenic Food Thesaurus (n = 4002), sold in Greece from 09/2020 to 01/2021, to map the prevalence of packaged foods sold under a ‘natural/organic’ claim and to compare their nutritional composition against food group matched conventional counterparts. Statistical analysis was carried out using IBM SPSS Statistics^®. Overall, ‘free from’ was the most commonly used claim (12.3%), followed by ‘natural/pure’ (9.1%), ‘fresh’ (4.6%), and ‘bio/organic’ (3.3%). Statistically significant differences between the nutritional composition of natural/organic and conventional foods were only found in 5 out of the 13 food categories and in 9 out of 39 subcategories. Being labelled as natural/organic was linked to improved nutritional composition for prepared foods and yogurts, while for breakfast cereal, there was a mixed effect with lower carbohydrate content but higher energy and fat content. Jams labelled as natural/organic had higher energy and total sugar content. Overall, evidence of an association between being labelled as natural/organic and having an improved nutritional composition was extremely rare.