Long-term organic amendments are a key strategy to build soil organic carbon (SOC) stocks in semiarid agroecosystems, where low biomass inputs and calcareous parent material constrain carbon accumulation. This 14-year field experiment in central Iraq (2000–2014) evaluated how a gradient of organic matter (OM) additions (0, 1, 2.5, 5, 10, and 20%) affects SOC dynamics, nutrient availability, and soil organic matter composition in clay-dominated, semiarid soils. Surface and subsurface samples (0–30, 30–60, and 60–90 cm) were analysed for SOC, nutrients, and mid-infrared Fourier transform infrared (FTIR) spectra, which were then integrated with Partial Least Squares (PLS) regression and RothC simulations. Moderate OM inputs (5–10%) were most effective in increasing surface SOC from 0.71% to 2.11%, while electrical conductivity, pH, and total nitrogen remained within agronomically acceptable ranges. FTIR spectra showed enhanced C–H and C=O bands in surface horizons, indicating concurrent accumulation of labile and more stable organic fractions, whereas low- and mid-wavenumber bands (1080–670 cm⁻¹) confirmed the persistence of clay and silicate mineral structures across depths. PLS models predicted SOC and total N with high accuracy (R² = 0.84–0.995), low RMSEP, and excellent predictive performance (RPD = 3.05–41), particularly under higher OM inputs. RothC simulations reproduced the observed depth-dependent SOC gradients, with deviations typically ranging from −22% to +10%, and confirmed that most carbon gains are concentrated in surface layers, while deeper horizons change only slightly. The combined use of FTIR spectroscopy, spectral PLS modelling, and RothC provides a robust framework for quantifying and predicting SOC responses to organic amendments in semiarid, calcareous soils. These findings highlight that sustained, moderate OM applications can substantially enhance SOC sequestration and soil fertility in degraded Iraqi soils, with broader relevance for semiarid agroecosystems worldwide.