Allergies and asthma have increased in prevalence over recent decades while the development of therapies to treat or prevent them has stagnated. Genetic predisposition and lifestyle changes influence the constituents of the microbiome and these host–environment–microbe interactions represent a key underlying pressure influencing disease susceptibility. Consequently, there has been a surge of interest in shaping the microbiome to a health-promoting state particularly through nutritional intervention strategies. However, mechanistic insights into the nutrition–microbe–host interplay are still needed in order for such approaches to succeed. In addition, little is known about how trans-kingdom interactions might influence disease susceptibility and progression. Future steps toward revealing the underlying mechanisms of host–microbe interactions will be pivotal for the development of effective dietary intervention strategies for the prevention and treatment of allergic diseases.