<p>Organic compost offers an environment for plant growth that is free from pests, undesirable microbes and weeds: ideal conditions for organic farming management. However, this environment generally lacks symbiotic soil fungi, such as arbuscular mycorrhizal fungi (AMF), and the mycorrhizal benefits of AMF. In this study, we aim to explore the impacts of inoculation of arbuscular mycorrhizal <i>Acaulospora</i> cf. <i>morrowiae</i> on tomato plant growth from the seedling stage to harvest and on the fungal microbiomes of organic substrates. The effects of AMF inoculation on tomato seedling growth were investigated in a sand mixture and an organic compost. Moreover, the effects on plant growth, yield and fungal communities of AMF inoculation in combination with vermicompost supplementation were elucidated using ITS2-amplicon sequencing at the flower to fruit development stage and harvest stage. <i>A.</i> cf. <i>morrowiae</i> did not colonize roots of five-week-old tomato seedlings grown in vermicompost and cocopeat. The fungus initiated hyphal colonization in 25% of tomato roots at the flower–fruit development stages in organic compost. The AMF successfully established a symbiosis with abundant arbuscules at the harvest stages. Thus, in fertile organic substrates, <i>A.</i> cf. <i>morrowiae</i> did not promote plant growth and yield but shaped endophytic and substrate fungal communities. The establishment of AMF symbiosis between <i>A.</i> cf. <i>morrowiae</i> and tomato is delayed in fertile organic substrates. AMF association did not promote growth and yield but altered fungal communities in tomato roots.</p> Graphical Abstract <p></p>