Nutrition-related mobile applications (apps) are commonly used to provide information about the user’s dietary intake, however, limited research has been carried out to assess to what extent their results agree with those from the reference method (RM). The main aim of this study was to evaluate the agreement of popular nutrition-related apps with the Polish RM (Dieta 6.0). The dietary data from two days of dietary records previously obtained from adults (60 males and 60 females) were compared with values calculated in five selected apps (FatSecret, YAZIO, Fitatu, MyFitnessPal, and Dine4Fit). The selection of apps was performed between January and February 2021 and based on developed criteria (e.g., availability in the Polish language, access to the food composition database, and the number of downloads). The data was entered by experienced clinical dietitians and checked by one more researcher. The mean age of study participants was 41.7 ± 14.8. We observed that all the apps tended to overestimate the energy intake, however, when considering the macronutrient intake, over- and underestimation were observed. According to our assumed criterion (±5% as perfect agreement, ±10% as sufficient agreement), none of the apps can be recommended as a replacement for the reference method both for scientific as well as clinical use. According to the Bland-Altman analysis, the smallest bias was observed in Dine4Fit in relation to energy, protein, and fat intake (respectively: −23 kcal; −0.7 g, 3 g), however, a wide range between the upper and lower limits of agreement were reported. According to the carbohydrate intake, the lowest bias was observed when FatSecret and Fitatu were used. These results indicate that the leading nutrition-related apps present a critical issue in the assessment of energy and macronutrient intake. Therefore, the implementation of validation studies for quality assessment is crucial to develop apps with satisfying quality.