Biocrusts are an essential soil surface cover at drylands where ecosystems are especially fragile to soil degradation processes due to climatic peculiarities. In the present work, (micro)biological and physicochemical properties indicative of soil functionality were studied in two different biocrust types dominated by Dipolschistes diacapsis and Lepraria isidiata and in underlying soil at two different depths (SL1, soil layer right below the biocrusts, and SL2, soil layer underlying SL1) at the Tabernas desert (southeast Spain). The influence of climatic factors (rainfall and temperature) and general soil properties on the (micro)biological properties were also analyzed in different environmental (climatic) conditions over a period of two years. PERMANOVA analyses showed significant statistical differences (Pseudo-F = 63.9; P (perm) = 0.001) among biocrust and soil layers. Throughout the study period, enzyme activities involved in C, N, and P cycles; microbial biomass-C; basal respiration; and several properties directly related to ecosystem productivity (total organic carbon, total nitrogen, concentration of ammonium and nitrate) were higher in both biocrust types than in the underlying soil layers, showing that biocrusts improved soil functions related to nutrient cycling. These properties progressively diminished in successive soil layers under the biocrusts (biocrusts > SL1 > SL2). Biocrusts showed greater similarity to each other and to SL1 than to SL2 in (micro)biological properties. A distance-based linear model analysis showed that total organic carbon, rainfall, pH, mineralized N-NH4+, and total nitrogen were the most important variables for predicting (micro)biological soil properties in biocrusts. Different biochemical behavior between the biocrusts and successive underlying soil layers has been found in wet periods. After rainfall periods, the biocrusts showed important peaks in basal soil respiration and in enzyme activities involved in C and P cycles. Nevertheless, soil biochemical properties hardly showed any peak in SL1 and did not change in SL2 despite soil moisture being higher in the soil layers below the biocrusts. Correlation analyses corroborated the existence of different relationships between soil moisture and enzymatic activities. In biocrusts, soil moisture showed a greater number of significant positive correlations with enzymes such as β-glucosidase, invertase, and phosphomonoesterase among others, whereas in SL1 it was only correlated with cellulase and in SL2 with dehydrogenase. A change in rainfall regime, as predicted by models based on climate change in arid and semiarid zones, could affect the activity of soil enzymes in the biocrusts and underlying layers, thus aggravating the degradation of these fragile dryland ecosystems.