<p>Affine processes play an important role in mathematical finance and other applied areas due to their tractable structure. In the present article, we derive probabilistic representations and integration by parts (IBP) formulas for expectations involving affine processes. These formulas are expressed in terms of expectations of affine processes with modified parameters and are derived using Fourier analytic techniques and characteristic functions. Notably, our method does not require pathwise differentiability, allowing us to handle models with square-root diffusion coefficients for a large set of parameters. The methodology can be applied to the classic Cox–Ingersoll–Ross (CIR) model, a model for interest rates in mathematical finance, where the initial value derivative corresponds to one of the “Greeks” used in option pricing in mathematical finance. Furthermore, we illustrate the theory with an application to a population evolution model arising as a scaling limit of discrete branching processes. Our approach offers a unified and robust framework for sensitivity analysis in models where classical Malliavin calculus techniques are difficult to apply.</p>