Pongamia pinnata (L.) Pierre, a fast-growing oil-seed-producing tree legume, has the ability to grow on wastelands. It can be utilized for biofuel plantation on such lands. The preconditioning of young seedlings during the early stage of development with efficient arbuscular mycorrhizal fungi (AMF) confers several benefits enhancing the possibility of their establishment in fields after outplanting from nurseries. However, before recommending these fungi for inoculation, the suitable AMF species must be identified. Therefore, to determine the potential AMF species, 9 purified fungi (isolated from different sites) were tested for their growth promotion activity. The inoculated fungi were not able to increase seedling growth. Some fungi reduced growth, which was attributed to more utilization of carbon by fungal symbiont. Development of fine roots was delayed up to 30 days after sowing and hence their colonization by AMF inoculants. This could be due to the large amount of nutrients stored in cotyledons of large P. pinnata seeds. Removal of cotyledons significantly reduced seedling growth and plants showed some extent of dependency on AMF inoculants. Thus, it was concluded that AMF inoculations should enhance biomass of P. pinnata only after depletion of metabolic reserves in its cotyledons and such mycorrhizal seedlings can be utilized for biofuel plantation.