A wide range of agroecology of Ethiopian soil is deficient in both major and micronutrients. The new fertilizer type for crop production is formulated based on the nutrient deficiency. This site-specific fertilizer does not show crop yield variability when compared with the previously recommended NP fertilizer. Understanding the most yield-limiting nutrient in crop production under different agroecology is very important. Hence, the objective of this study was to identify the most yield-limiting nutrient and quantify the level of yield penalty in maize crops under three locations in the Yeki district during the 2022 cropping season. Ten treatments constitute of control, RNP, RNP +S2, NPKSBZn, PKSBZn (-N), NKSBZn (-P), NPSBZn (-K), NPKBZn (-S), NPKSZn (-B) and NPKSB (-Zn) were arranged by randomized complete block design under three replication. Maize agronomic data were taken and analyzed by using R software 4.2.2. The mean difference of treatments was compared by LSD at a probability level of 5%. The pool means analysis of variance indicated that maize grain yield and yield components were significantly (p<0.05) influenced by different nutrient omissions. The highest maize grain yield penalty (41.34%) was recorded under the nitrogen omitted plot and the lowest (0.65%) from the previously recommended NP fertilizer applied plots. In the study area the most yield reduction that showed more than 10% yield penalty of maize 26.25%, 22.13% and 11.26% due to S, P and K omitted respectively were observed next to N. Since the study was conducted for one season further validation and demonstration for specific nutrient across multi-location and soil test based will be better to see more variability.