The progressive development of clinical and public health nutrition has long relied on dietary clinical trials (DCTs), investigating the causal relationship between diet and multiple risk factors of non-communicable and chronic diseases. DCTs are also hallmarks for establishing dietary requirements and promoting overall nutritional health among the population. Despite their critical importance in translation into public health strategies and practices, DCTs have several limitations and challenges for study design, implementation and finding interpretation. The complex nature of nutrition interventions, collinearity between diet components, multi-target effects of the interventions, diverse dietary behaviors, and food culture are the most challenging issues. Furthermore, baseline exposure and dietary status, appropriate control groups, blinding, randomization, and poor adherence undermine the effectiveness of DCTs in translation into practices. Disruptive factors will be minimized if researchers are committed to following good clinical practice (GCP) standards available for common designs of clinical trials. Planning DCTs, however, needs careful considerations for hypothesis generation, study design development, the definition of primary and secondary outcome measures, and target population.