The increasing cost of fuel and machinery used in conventional tillage systems makes no-till management (NT) an enticing alternative for small-grain producers. However, the application of fertilizers to the soil surface under NT has been shown to lead to the stratification of pH and other soil acidity parameters near the soil surface. Despite that, only a few works have reported the soil acidity stratification of the arable layer and were restricted to highly weathered acid soils of the tropics. Therefore, our objective was to quantify soil pH, exchangeable aluminum (AlKCl), aluminum saturation (Al%), soil organic carbon (OC), and cation exchange capacity (CEC) by depth in the topsoils across different levels of nutrient management in three long-term continuous NT wheat studies in the southern Plains of US. Plots were sampled after the winter wheat (Triticum aestivum L.) harvest in the summer of 2019 at sampling depths of 0–15 cm, and 0–2.5, 2.5–5, 5–7.5, 7.5–10, 10–12.5, and 12.5–15 cm. Treatments included an unfertilized check and a combination of increased rates of nitrogen (N) in addition to phosphorus (P) and potassium (K) application across all study locations. It was found that stratification occurred for all soil acidity parameters tested in the study, with higher OC and AlKCl, and lower pH near the soil surface. Patterns of soil pH and OC stratification were generally related to the rate of annual N fertilization. The long-term N fertilization significantly reduced soil pH in the topsoil (0–15 cm) and stratified soil layers, especially at the higher application rates. Regardless of the soil sampling depth, pH decrease was significantly related to the amount of N applied. Also, N fertilization significantly increased AlKCl and Al% but decreased the sum of Ca2++Mg2++K++Na+ both in the whole topsoil or layers. AlKCl and Al% were increased exponentially and linearly with increasing N rate and were for 0–15 cm and stratified layers, respectively. AlKCl was exponentially (inversely) related to soil pH for both sampling methods. Nitrate (NO3) was inversely related to soil pH until up to 21.9 ± 2.6 mg NO3N kg−1. Although not at the same magnitude, non-fertilized plots were likewise stratified for the tested parameters, which indicates other effects of NT on the stratification rather than the fertilizer addition. Overall, the buffer index (BI) was lower if the soil is sampled from 0 to 2.5 cm than 0–15 cm. Attention regarding sampling depth in NT areas is essential for accurate soil attributes monitoring.