AbstractNitrification inhibitors, such as nitrapyrin (NI), are increasingly co‐applied with nitrogen (N) fertilizers as part of sustainable agricultural practice. Several studies in temperate regions have documented the effectiveness of NI in retaining soil ammonium (NH4+), minimizing N loss and increasing crop yields. However, less is known about the effects of NI in Mediterranean regions, where agricultural production is challenging and requires intensive irrigation and fertilization. We investigated the short‐term impact of the nitrification inhibitor nitrapyrin (2‐chloro‐6‐(trichloromethyl)pyridine) in a two‐factor mesocosm experiment, using a typical Mediterranean soil, where NI was co‐applied with a selection of urea‐based fertilizers: urea (U), U with urease inhibitors (U + UI), methylene urea (MU) and zeolite‐coated urea (ZU). NI co‐applied with urea fertilizers resulted in higher availability of soil NH4+ and a concurrent increase in NH3 volatilization. Net cumulative soil NH4+ availability was 1.5–3.3 fold greater when NI was applied. Concurrently, net cumulative nitrate (NO3−) and nitrite (NO2−) availability was reduced by 10%–60%; this was found for all the tested fertilizer types except MU fertilizer, where the net cumulative soil NO3− and NO2− doubled. Nitrous oxide (N2O) emissions from urea fertilization were reduced by 40% with UI, 50% with NI and 66% with NI + UI. Interestingly, after 28 d, the composition of soil microbial communities was distinctly different, due to NI application. Specifically, NI application dramatically reduced the abundance of ammonia‐oxidizing and denitrifying bacterial functional groups. NI was effective in reducing N2O emissions in this calcareous soil; however, NH3 emissions were remarkably enhanced. These findings have important implications for the large‐scale adoption of inhibitor technologies in Mediterranean agroecosystems and for the reduction of greenhouse gas emissions.