Humus is a central and relatively stable component of soil organic matter that regulates key fertility functions; therefore, robust evaluation of humus dynamics requires long-term stationary experiments. This study synthesizes results from long-term irrigated experiments on light chestnut soil in southeastern Kazakhstan (single-factor experiment, 1961–2005; multifactor experiment, 1991–2016) together with renewed environmental monitoring (2020–2023) to quantify the effects of mineral fertilization and cattle manure on humus status, plant-available nutrients, crop productivity, and environmental safety. Under continuous cropping without fertilizer input, humus in the 0–20 cm layer declined by 0.37 percentage points relative to the initial level. Mineral fertilization alone moderated humus loss but did not ensure a non-deficit humus balance, whereas combined organic–mineral fertilization (NPK + manure 60 t ha⁻¹ once per rotation) increased humus by 0.20 percentage points, reaching 2.80% by the end of the fifth rotation. Fertilization substantially improved nutrient status: under mineral fertilization, available P₂O₅ and exchangeable K₂O reached 39.5 mg kg⁻¹ and 601 mg kg⁻¹, respectively, while under the combined system they reached 52.3 mg kg⁻¹ and 765 mg kg⁻¹. Regression models from the multifactor experiment quantified dose–response relationships between fertilizer/manure inputs and soil indicators. In the fifth rotation, yields of winter wheat, maize, and alfalfa increased by 1.4–2.0 times relative to the unfertilized control, while sugar beet yield increased more than threefold. Soil heavy metal concentrations remained below sanitary–hygienic thresholds across treatments; however, lead (Pb) in maize grain exceeded the maximum permissible concentration across all fertilization systems, indicating the need for continued product monitoring and source/pathway evaluation.