The environmental experience of plants can modulate the development of the offspring and their interactions with other organisms. These effects, generally known as maternal effects, occur through seed provisioning and epigenetic modifications. This study considers the influence of differing environments of maternal plants on their progeny and their biotic interactions. Seeds were collected from two Eucalyptus grandis clonal seed orchards having different abiotic and biotic conditions. Seed and seedling development, and seedling responses to pest infestation and pathogen inoculation were measured. Finally, fungal communities in the foliage of the seedlings were assessed using a metabarcoding approach. The percentage of seed germination and height of seedlings were influenced by the maternal environments. Seedlings from one of the maternal environments were significantly more resistant to a pathogen than seedlings from the other. The composition and diversity of fungal communities also differed between the offspring from the two maternal environments. We found that the differences in the maternal environment affected the progeny performance and resistance. Moreover, we show for the first time that the maternal environment can influence the structure of fungal communities in the foliage in the subsequent generation.