The intensive use of wood resources is a challenging subject around the world due to urbanization, population growth, and the biodegradability of wooden materials. The study of the climatic conditions and their effects on biotic wood degradation can provide a track of trends of wood decay and decomposition at regional and global scales to predict the upcoming responses. Thus, it yields an overview for decision-makers and managers to create a precise guideline for the protection of wooden structures and prolonged service life of wooden products. This study aimed at investigating the decay hazard in Iran, its decadal changes, and how it is affected by different phases of the El Niño Southern Oscillation (ENSO). Therefore, the risk for fungal decay of wood was estimated based on the Scheffer Climate Index (SCI) at 100 meteorological stations located in Iran, for the period 1987–2019 (separately for first, second, and third decade as decadal analysis). Subsequently, SCI value trends were analyzed using the Mann–Kendall and Sen’s slope method. Finally, the relationship between SCI and climatic parameters (temperature and precipitation) was explored. Generally, the SCI fluctuated between 2 and 75 across the region. The decay risk was ranked as low in most parts, but moderate in the northern part of the country along the Caspian Sea coastlines. Decadal analysis demonstrated that the highest mean SCI values took more place in the third decade (58% of stations) and the lowest mean SCI values in the second decade (71% of stations). Furthermore, the highest and the lowest SCI values occurred at 70 and 66% of stations in El Niño and Neutral phase, respectively. Trend analysis of SCI values showed that large parts of several provinces (i.e., Markazi, Tehran, Alborz, Qazvin, Zanjan, Ardebil, East Azarbayjan, West Azarbayjan, Kurdestan, Kermanshah, and Ilam) exhibited a significantly increasing decay hazard with a mean SCI of 2.9 during the period of 33 years. An analysis of causative factors (climatic parameters) for these changes revealed that all the meteorological stations experienced a significant increase in temperature while the number of days with more than 0.25 mm precipitation increased at some stations but decreased at others. However, in summary, the SCI increased over time. Hence, in this study, the effect of precipitation on SCI was confirmed to be greater than the temperature. Analysis of the results shows that the correlation between the SCI and ENSO was positive in most of the stations. Moreover, the results of spectral coherent analysis of SCI and ENSO in different climates of Iran showed that the maximum values of SCI do not correspond to the maximum values of ENSO and are associated with lag time. Therefore, the extreme values of the SCI values cannot be interpreted solely on the basis of the ENSO.