The nutrient quality of 96 beverages in Sweden was assessed based on the Keyhole (KH), Nutri-Score (NS) and Nutrient Rich Food (NRF) index. Of milk- and plant-based beverages, 20% were similarly rated by all three as either high or low quality. Keyhole evaluated plain milk more coherently to the dietary guidelines, whilst NS assessed plant-based beverages more consistently than other indicators. Of water-based beverages, 61% were similarly rated by NS and NRF, with highest alignment in sugar-sweetened and non-nutritive sweeteners containing beverages. According to NS, water, unsweetened beverages, freshly squeezed fruit juices and vegetable juices qualified as nutritious choices. NRF index evaluated beverages less coherently to the guidelines and the rating of products largely mirrored fortification. Thus, agreement among indicators varies across beverage groups. NS is suitable to rate the nutrient quality of most beverages consistently with the dietary guidelines, except for milk where KH outperforms NS.