Major objectives of this study were to evaluate the effects of organic, conventional and integrated orchard fruit production systems on the quality and quantity of soil organic matter in orchard floors and to identify sensitive soil organic matter indicators. Seventeen different soil organic matter parameters were studied. These were soil aggregate stability (AS), total nitrogen (TN), total carbon (TC), carbon/nitrogen ratio, microbial biomass N (BN), microbial biomass C (BC), BC:BN; BC:TC; BN:TN; hot-water extractable C (HC), hot-water extractable carbohydrate (HCA), HCA:HC; humin N (hum N), humin C (hum C), hum C:TC; hum N:TN and potentially mineralizable N (Pot N). They were based largely on soil organic matter characteristics and fractions extracted sequentially by different extractants from soils collected from the alleys and treelines of organic, conventional, and integrated grassed-down apple orchard types from both commercial and experimental sites in Canterbury, New Zealand. A total of 12 apple orchards were investigated. Soil samples collected from these orchards (0–75 mm depth) were analysed for TC, TN, BC, BN, Pot N, AS and also sequentially extracted for labile and stable soil organic matter fractions using cold and hot water, acid mixtures (hydrochloric:hydroflouric acids, HC1:HF) and alkalis (sodium pyrophosphate and sodium hydroxide, Na4P207and NaOH). Only TN, BN, and BN:TN showed significant interaction effects and all these were associated with soil N. Overall, combining orchards according to similar management systems, results obtained showed no significant differences between experimental and commercial orchards. However, sensitive indicators capable of distinguishing significant differences between different orchard management systems were BC, BC:TC and HCA:HC while HCA:HC distinguished significantly between treelines and alleys within each group of the same orchard type.