Accurate dietary analysis of energy, nutrient intake, and meal timing in human studies using traditional dietary assessment methods (e.g., food records) is challenging and time-consuming. The widespread use of smartphones, tablets, and nutrition applications (apps) can overcome some of these problems. The objective of this study was to evaluate the validity of an FDDB smartphone app and food database compared with PRODI^®—a professional platform for nutritional counselling using the German Nutrient Database. Dietary records were collected from 10 subjects participating in the crossover intermittent fasting trial for 2 weeks at baseline and during the eating timeframe of 8 h (early or late in the course of the day). The FDDB app and database enabled a quicker and less sophisticated analysis of food composition and timing than the PRODI^® software. Good agreement between the methods was found for energy and macronutrient intakes, while the FDDB data on most micronutrients and saturated/unsaturated fat intake were unreliable. In contrast to PRODI^®, FDDB provided effective assessment of timely compliance, making it a promising tool for chrononutritional studies. Thus, the FDDB app is comparable to the traditional PRODI^® dietary assessment method, and can be effectively used in human dietary trials and medical practice for specific goals.