There is a paucity of information on the efficacy of nutrient amendments made from readily available local material on seedling quality. The objectives of this study were to evaluate the combinatory effects and relationships of compost tea, fertiliser, and Glomus intraradices inoculated-substrate on tomato seedling quality as defined by fresh and dry biomass, root to shoot ratio, length of root and stem, and selected root system architecture parameters. The factorial designed assays consisted of tomato sown in autoclaved or non-autoclaved peatbased substrates, which was either fortified (PM) or not fortified (PNM) with the endomycorrhizal fungi, G. intraradices, to which fertiliser only (FO), unfiltered compost tea + fertiliser (UCT + F), or filtered compost tea + fertiliser (FCT + F) were applied to these substrates. With the exception of the positive effect of FCT + F on leaf area, the application of compost teas + fertiliser to PM substrates (nonautoclaved or autoclaved) did not provide any additional benefits compared to FO treatment. However, FO applied to PM or autoclaved substrates resulted in lower or lowest seedling growth (root and shoot) compared to UCT + F applied to PM substrates. The application of FCT + F, which had similar nutrient supplying capacity as UCT + F but without microorganisms, to PM substrates, resulted in significantly lower seedling growth. Roots were not colonised with G. intraradices and results suggest that increased seedling growth was related to the biological properties of the UCT and non-autoclaved substrates. Network width to depth ratio was the most important factor affecting shoot growth. Quality of tomato seedlings resulting from non-autoclaved PM and PNM substrates applied with UCT + F was comparable.