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This work assessed, under nursery conditions, the effect of arbuscular mycorrhizal fungi (AMF) inoculation on the initial growth of the woody species Heliocarpus popayanensis Kunth in containers of different sizes (nursery tubes of 50 or 250 cm3) containing composted cattle manure or organic Pinus spp bark compost diluted (0 to 100%, each 9%) with low fertility soil. Plants in cattle manure grew more than plants grown in pine bark manure independent of tube size. AMF were more efficient in improving plant growth in 250 cm3 tubes than in 50 cm3 tubes independent of the substrates. Mycorrhizal plants grown in 50 cm3 tubes showed less growth than non-mycorrhizal ones irrespective of the substrates. Nevertheless, this growth depression decreased with an increase of substrates dilution with low fertility soil. In the higher dilutions, growth depression did not occur and there was a positive response to AMF inoculation. In addition, only mycorrhizal plantlets showed some growth in low fertility soil as the sole substrate. These results indicated that AMF affect plantlet growth positively or negatively depending on the combination of substrates, fertility level, and container size.