Improving the efficiency of agricultural enterprises in Kazakhstan requires a comprehensive accounting of production, financial, technological, and risk factors, since an increase in nominal output does not always reflect a real improvement in performance. The aim of this study is to develop an economic-mathematical model for the quantitative assessment and forecasting of the effective development of agricultural enterprises in Kazakhstan amid a growing innovation-driven economy. The information base was compiled using official statistical data of Kazakhstan for 2010-2025 on gross agricultural output, volume indices, gross harvest and yield of grain and leguminous crops, the introduction of water-saving technologies, and technical modernization of the industry. The methodological framework combines indicator standardization, entropy weighting, an innovation- and risk-augmented production function, an optimization formulation for resource allocation, and scenario-based forecasting of an integral efficiency index. The results showed that in 2019-2025, nominal agricultural output increased by 88.5%, while the real physical volume increased by about 24%. In 2025, the yield of grain and leguminous crops reached 16.31 c/ha, exceeding the previous year’s level by 7.2%. In the innovation scenario, the profit of a conditional enterprise increases by about 28.6%, and the return on costs increases from 53.85% to 67.22%. By 2030, the value of the integral index in a given innovation scenario reaches 140.26 points versus 110.41 points in the inertial scenario. The results obtained can be used in intra-company planning, evaluation of investment decisions, and monitoring the effectiveness of agricultural policy.