The purpose of the study was to investigate the effect of clinoptilolite zeolite and vermiculite on (i) nitrogen (N) and phosphorous (P) acquiring enzymes' activity, (ii) potential nitrification rate (PNR), and on (iii) availabilities of the inorganic N forms. These parameters are critical to description of N mineralization and nitrification processes regulating the fate of N in agricultural ecosystems. A time-course (60-days) microcosm study was conducted on a circumneutral agricultural soil, where clinoptilolite zeolite and vermiculite were added as a mixture with N substrate (i.e., urea or manure). Zeolite inhibited urease activity regardless of the N supply (manure or urea). On the contrary, the activities of acid phosphatase, alkaline phosphatase, N-acetylglucosaminidase (NAG), asparaginase, glutaminase, and arylamidase remained unaffected. Moreover, zeolite and vermiculite affected the NH4+ availability and retarded the NO3- accumulation in the soil, by 22 and 25%, respectively. Zeolite and vermiculite amendments showed lower potential nitrification rate (PNR) than single urea ones, by 58 and 45%, respectively, at day 15. Clinoptilolite zeolite and vermiculite affected nitrification activity and potentials of soil under organic and inorganic N amendment, whereas zeolite inhibited urease activity, suggesting an influence on the overall biochemical cycle of N. Further work is needed to elucidate as follows: (i) the responsible mechanism(s) behind the inhibited urease activity, (ii) the response of decomposing and nitrifying microorganisms, and (iii) the implications on N transformation rates.