Composting is an effective strategy to process agricultural and urban waste into forms that may be beneficial to crops. The objectives of this orchard field study were to characterize how a dairy manure compost and a food waste compost influenced: (1) soil nitrogen and carbon pools, (2) bacterial and nematode soil food webs and (3) tree growth and leaf N. The effects of composts were compared with fertilized and unfertilized control plots over two years in a newly planted almond orchard. Both dairy manure compost and food waste compost increased soil organic matter pools, as well as soil nitrate and ammonium at certain time points. Both composts also distinctly altered bacterial communities after application, specifically those groups with carbon degrading potential, and increased populations of bacterial feeding nematodes, although in different timeframes. Unique correlations were observed between nematode and bacterial groups within compost treatments that were not present in controls. Food waste compost increased trunk diameters compared to controls and had greater relative abundance of herbivorous root tip feeding nematodes. Results suggest that recycled waste composts contribute to biologically based nitrogen cycling and can increase tree growth, mainly within the first year after application.