- Trees in forests and shrubs in shrublands can be considered physical ecosystem engineers since they modify their environment by creating patches that differ in their ecosystem properties from un-engineered patches. The objective of this study was to evaluate the effects of replacing one functional group of woody species (shrubs) with another group (trees) that differs in its ecosystem engineering (EE) mode on soil and vegetation as emerging ecosystem properties in the northern Negev, Israel. The soil quality index (SQI) and the aboveground net primary productivity (ANPP) of herbaceous plants were used as emergent ecosystem properties for characterizing woody and non-woody patch states. The SQI integrates 14 physical, biological, and chemical soil properties, indicating the soil state in a patch. The ANPP of herbaceous plants was estimated as the annual plant biomass accumulation, indicating the vegetation state in a patch. Relationships between the SQI and ANPP properties in different patch states were calculated in terms of the magnitude (MG) and direction of the change (θ). The results show an overall conservation of the collective ecosystem properties on the landscape level, but an inversion in the ecosystem functions of the two patch types arising from the replacement of the woody EEs. A significant correlation between SQI and ANPP was found in the forest and shrubland system, with R2 = 0.89 and R2 = 0.82, respectively. In the forest, higher SQI and herbaceous plant ANPP scores were found in the non-woody patches than in the tree understory with MG = 0.27 and θ = 214.61. The opposite trend existed in the shrubland where higher SQI and ANPP scores were found under the shrub canopy than in the non-woody patches with MG = 0.34 and θ = 43.65. The conclusions are: (1) the engineering properties induced by the dominant woody plants through patch formation are important in driving ecosystem modulation; (2) the SQI and ANPP trajectories represent the magnitude of change between patch type, and (3) SQI and ANPP are reliable emergent ecosystem properties for evaluating changes of patches formed by woody plants as EEs.