Soil management practices significantly impact soil aggregation and carbon (C) dynamics. Organic fertilizer and mycorrhizal inoculation also affect aggregate stability and soil C pool. Thus, this study was designed to assess the effects of inorganic and organic fertilizer treatments (control, chemical fertilizer, animal manure, compost, and compost + mycorrhizal inoculation) on bulk density (ρ b ), C and N concentrations, soil organic C (SOC) pool, C sequestration, total N, aggregate fractions, water-stable aggregates (WSA), and mean weight diameter (MWD) in the long-term field experiment initiated in 1996 on the Mediterranean coast of Turkey. Disturbed and undisturbed soil samples were collected from the 0- to 0.15-m and 0.15- to 0.30-m depths after wheat (Triticum aestivum) harvest in June 2010 to determine the soil physical and chemical characteristics. Soils that received animal manure, compost, and compost + mycorrhizae contained more C (in percent), N (in percent), SOC, and total N concentrations than control. In comparison with control, chemical fertilizers also affected soil C and N concentrations and pools by increasing plant biomass production. The C/N ratio of soil was less than 10 in control and chemical fertilizer treatments but more than 10 in animal manure, compost, and compost + mycorrhizae treatments. Organic fertilizers significantly reduced ρ b and increased porosity (in percent). Total amounts and rate of C and N sequestration increased with application of organic fertilizers. The rate (kg C ha ―1 year ―1 ) of C sequestration in 0- to 0.15-m depth was 7.19 for control, 329.6 for animal manure, and 273.4 for the compost + mycorrhizae treatment. Furthermore, organic fertilizers significantly increased the SOC concentrations in different aggregate size fractions. The C and N concentrations in the 0.25- to 1.0-mm aggregate size were higher than those in the less than 0.25-mm fraction. Concentrations of C and N decreased significantly with the decrease in aggregate size less than 0.25 mm (P < 0.0009). Application of organic fertilizers impacted soil ρ b , WSA, and MWD. Compost + mycorrhizae―treated soil had the highest MWD (3.09 mm), and the control treatment had the least (1.49 mm). Decline in aggregate size decreased WSA in compost and mycorrhizae treatments. The high values of MWD were associated with mycorrhizal inoculation rather than with application of organic fertilizer. Application of organic fertilizers including mycorrhizal inoculation contributed considerably to soil aggregation and soil C sequestration. There was more C concentration in 1- to 2-mm and 0.5- to 1-mm aggregate sizes than in the less than 0.25-mm size range. Additional research is needed to assess the role of mycorrhizae on macroaggregate development and C sequestration under long-term soil and crop management systems.