Excessive sugar intake and the associated increased obesity risk indicate that food reformulation is needed. Non-alcoholic beverages are often high in free sugars, making reformulation with low and no-calorie sweeteners (LNCS) a common choice. Our knowledge of the use of LNCS in the European food supply is, however, very limited. This study aimed to evaluate the trends in the use of LNCS in different non-alcoholic beverages in the Slovenian food supply over the course of two years. We assessed which LNCS are most used and how the use of LNCS affects energy and sugar content. We analyzed labeling information of non-alcoholic beverages in selected grocery stores, covering the majority of the Slovenian food supply. Selected grocery stores were located in the capital city (Ljubljana). LNCS were present in 13.2% and 15.5% of non-alcoholic beverages in the years 2017 and 2019, respectively. The use of LNCS has significantly increased only in energy drinks (p < 0.01). The most used LNCS in 2017 were acesulfame K, aspartame, and cyclamates. In 2019 the use of sucralose increased significantly (p < 0.01) to become the second most used LNCS. Energy and sugar content varied between subcategories, which depended on the presence of added sugar and LNCS. Comparison between the energy value and the presence of the LNCS showed an almost 50% lower energy content of beverages containing both added sugar and LNCS (E2017 = 92.8 kJ; E2019 = 96.2 kJ per 100 mL), compared with beverages with only added sugar (E2017 = 161.8 kJ; E2019 = 159.0 kJ per 100 mL). In beverages sweetened only with LNCS, the difference was even more noticeable (E2017 = 22.3 kJ; E2019 = 14.3 kJ per 100 mL). Results show that the use of LNCS can help producers reduce the energy value of non-alcoholic beverages. Still, compared to other countries, the offer of such products in the Slovenian food supply is relatively low. However, due to possible public health risks of excessive use of LNCS, producers should be further encouraged for reformulation and production of less sweet products without LNCS, enabling consumers to adapt to less sweet taste of beverages. Further monitoring of LNCS in the food supply is therefore recommended, preferably also with consideration of sales data.