Investigating soil pipes and pipe collapses that lead to gully headcut formation, and considering the role of biological activities leads to a better understanding of soil erosion processes. Soil organisms and animal activities can both increase soil erosion by creating underground tunnels that may lead to the formation of soil pipes, and decrease it by reinforcing plant presence, soil porosity, and soil stability as a result of their mixing activities. The main aim of this study was to assess the role of plant and animal species on soil pipe formation in a semi-arid region affected severely by piping and gully erosion. The study was conducted in the Sarakhs Plain, in the Razavi Khorasan Province in Iran. Four study sites were selected: a slope with erosion (i.e., gully headcuts and pipe collapses), a slope without erosion, a location with dominant plant species (i.e., Artemisia annua, Camphorosma monspeliaca), and a location with dominant animal species [i.e., Formicidae (ants), termites, and Libycus Merio]. Four groups of methods were applied: bioecological tests (microbial respiration and biomass, ecological stoichiometry, and spatial point pattern analysis), geophysical test (ground penetration radar—GPR), geochemical–microscopic tests (scanning electron microscope—SEM, energy-dispersive X-ray—EDX, microanalysis TIN section, X-ray diffraction), and pedological analyses (doing soil profiles in the field and laboratory analyses of physical and chemical properties of soil samples taken in the field) to design models which can help to explain the formation of closed depressions, underground tunnels, and gully headcuts. The results showed that wherever the microbial respiration was increased, the greater the number of underground tunnels was formed. In the case of ecological stoichiometry, there was a significant difference between the slope without erosion and other test locations. The positive relationship between soil piping and biological activities was proved by bivariate pair correlation tests. The effects of soil organisms on piping were positively recognized using GPR. The results of EDX in the slope with erosion showed the presence of SiO2 and Al2O3, although there were small amounts of Na (Albite) and Ca (Wollastonite) in regions with dominant animal species, and K (MAD-10 Feldspar) in regions with dominant plant species. The TIN section made on the slope with erosion showed high silt content in comparison with the slope without erosion. The physical and chemical soil properties in four test groups, using the Duncan statistical test, showed the highest levels of significance in silt content, calcium carbonate, and bulk density. Finally, we have presented models of soil piping processes resulting from the action of living organisms. We confirmed a complex relationship between biological activity and soil pipe formation underlining the need for further interdisciplinary research on these relationships to better understand land degradation processes. [ABSTRACT FROM AUTHOR]