This research is a two year study on the effects of endomycorrhizae on vegetable production using conventional vs. organic practices. Objective of this study was initiated to determine if mycorrhizae improve yield, available soil nutrients and soil quality from two different fertilizer sources. Measurements were taken on yield, available soil nutrients, and soil quality in comparison of glomalin production and soil loss percentage. Two plant species were chosen, Tomatoes (‘Big Beef’) and Bush Beans (‘Tenderette’). A randomized split block 2 x 3 factorial treatment arrangement was used with two crops and three different inputs: Mo- 0 mycorrhizae, M1- recommended rate, and M2- 2x recommended rate of mycorrhizae. Each mycorrhizal input was replicated three times in both the conventional and organic system. Results show there was no difference in yield based on mycorrhizae additions at any rate. There was a significant yield difference based on conventional production over organic production in tomatoes and snap beans in 2010 and tomatoes in 2011. Possible explanations for yield difference in the organic production system include: different insect controls and a slower release of nutrients from poultry litter. Available soil nutrients were not influenced in the study based on mycorrhizal inputs in inorganic or organic tomato production. Soil available nutrients were significantly influenced in organic tomato when compared to inorganic tomato production at selected sampling dates. Mycorrhizae did not influence soil fertility in inorganic snap bean or organic snap bean production. Soil available nutrients were significantly influenced in organic snap bean when compared to inorganic snap bean production at selected sampling dates. Glomalin production and soil loss percentage were not shown to be significantly different within organic or inorganic treatments based on mycorrhizae inputs. However, glomalin production was shown to be significantly greater in organic production compared to inorganic in 2011. An explanation of this could be due to the use of leaf mulch as organic weed control. Although a numerical decrease was observed in soil loss percentage in organic production compared to inorganic production from the first year to the second, it was not shown to be a significant amount.