Traditionally, three threshold levels have been accepted for heavy metal concentrations in agricultural soils, depending on soil pH. The aim of this work was to ascertain how the three threshold values proposed for Cd (3, 6.5, and 12.5 mg kg−1) and Zn (300, 650, and 1300 mg kg−1) really affect soil microbial activity. Two soils, a scrubland soil and a forest soil, differing widely in their organic C content, were used in this study. Despite the different soil characteristics, the fractions of Cd and Zn extracted with a solution of diethylenetriaminepentaacetic acid (DTPA) showed little difference between soils. Parameters, such as microbial biomass C (Cmic), soil basal respiration (BR), adenosine triphosphate (ATP) content, dehydrogenase activity (DHA), urease activity (UA), alkaline phosphatase activity (APA), and β-glucosidase (β-GA), were less affected by heavy metals in the forest soil than in the scrubland soil. In general, the simultaneous addition of both metals had a synergistic effect on microbial activity, and this treatment produced a significant decrease of microbial activity of both soils with respect to control. The highest level (L3) of Cd, Zn and Cd + Zn treatments produced significant decrease of microbial and biochemical parameters in both soils.