A modified in-growth core technique was employed to determine the contribution of indigenous arbuscular mycorrhizal fungi (AMF) to plant growth and nutrient uptake in intensive agroecosystems at two Experimental field sites at Shangzhuang (Experiment I) and Quzhou (Experiment II) in North China. The growth cores (26.5 cm depth, 5 cm diameter for maize plants, and 4 cm for alfalfa and tomato plants) were covered with 40-μm nylon mesh (restriction of hyphal growth) and buried in the soil. They either remained static (static mesh) or were regularly rotated (rotated mesh) to disrupt hyphal penetration into the cores. A non-rotated 0.45-μm mesh (block mesh, inhibition of hyphal growth) treatment which remained static was also included to compare with the rotated mesh treatment (Experiment I). Growth cores from the two experimental sites had different soil types and two contrasting low P levels. The soil in the growth cores was sieved and sterilized before being placed into the growth core. Three plant species, namely maize, tomato and alfalfa were selected. The growth periods for maize plants were 35 days (Experiment I) and 39 days (Experiment II), respectively, and the corresponding growth periods for tomato and alfalfa were 67 days (Experiment I) and 53 days (Experiment II). At harvest the AMF species inside and outside the in-growth cores were identified by polymerase chain reaction (PCR), cloning and sequencing. Irrespective of plant species or genotype (maize), root colonization rates and hyphal length density (Experiment I) were generally suppressed in the rotated mesh treatment. The inhibition of hyphal growth by block mesh was comparable to that by the rotated mesh treatment. The growth of all three plant species in static mesh at the two Experimental sites, at both low (Experiment I) and sub-optimal soil P supply levels (Experiment II), was significantly higher than in the rotated (or block mesh) treatment. Root colonization rates of three maize genotypes were positively correlated with plant P concentration (Experiment II). Uptake efficiencies of P and N were significantly higher in static mesh than in the rotated (or block) treatment. AMF species detected (Experiment I) were all Glomerales, including the genera Glomus and Rhizophagus. One identified species of Rhizophagus intraradices and one Glomus viscosum-like phylotype were the dominant species. We conclude that the indigenous AM are crucial for early seedling growth, particularly for plants with small seeds and low P reserves and when seedlings exhibit P deficiency. The facilitation effect is highly relevant to enhanced root P (and possibly N) uptake and P delivery by the fungal mycelium. Our results have implications for the importance of maintenance of intact hyphal networks in intensive agroecosystems.