To increase teenagers’ nutrition knowledge is an important target and has the potential to improve their dietary habits and lifestyle while reducing incidences of obesity-related non-communicable diseases throughout the whole lifespan. This study protocol presents the general approach and details of an assessment of nutritional knowledge, attitudes toward nutrition, diet quality, lifestyle and body composition that have been used to comprehensively evaluate the cross-behavioral patterns covering dietary and lifestyle behaviors in Polish teenagers. The study was designed in two paths as: a cross-sectional study (covering 1569 students) and an education-based intervention study (464 students) with a 9-month follow-up. We describe a short form of the food frequency questionnaire (SF-FFQ4PolishChildren) used to collect data and details of diet-related and lifestyle-related education program, which was developed and implemented by academic researchers involved in the study. We also describe details of the data development and statistical analysis, including multidimensional methods of clustering variables to identify cross-behavioral patterns covering diet and lifestyle. The results of the study will provide evidence-based support for preventive health care to promote normal growth and development of young population and reduce the risk of diet-related diseases in adulthood, by early shaping of adequate dietary and lifestyle behaviors. In the future, well-tailored education programs addressed to teenagers can be created as an important public health action, based on our results.