According to the literature and our own research, damage to organically produced potted plants with peat-reduced growing media is related to high ammonium levels. The investigations carried out to date have related the damage mainly to two causes: i) ammonium toxicity as a consequence of the transformation of organic N in organic fertilizers to ammonium and ii) the formation of ammonia, a toxic gas at small concentrations, from ammonium caused by pH levels above 7 in the culture medium. However, these causes are only able to explain a proportion of the cases and until now the exact cause of the damage has not been found. For this reason, it is possible that the high ammonium contents are only an indicator of the presence of phytotoxic compounds that cause damage to the plant and, at the same time, inhibit nitrification. Similar to what happens in the composting process, these compounds can be metabolites of organic matter degradation processes. It is for this reason that the ammonium to nitrate ratio is an important parameter to determine the maturity of the compost. It has been discovered that multiple microorganisms that participate in the organic matter degradation process are also producers of metabolites with phytotoxic action. Furthermore, research shows that the production of these compounds is highly dependent on the N source available for uptake by microorganisms. Thus, the production of phytotoxic compounds can be favored by a high ammonium content in the culture medium. Our hypothesis is that these microorganisms would be, on the one hand, causing damage to the plant and, on the other hand, inhibiting nitrifying agents, which explains the high ammonium contents.