We initiate the study of spectral sparsification for instances of Constraint Satisfaction Problems (CSPs). In particular, we introduce a notion of the \emph{spectral energy} of a fractional assignment for a Boolean CSP instance, and define a \emph{spectral sparsifier} as a weighted subset of constraints that approximately preserves this energy for all fractional assignments. Our definition not only strengthens the combinatorial notion of a CSP sparsifier but also extends well-studied concepts such as spectral sparsifiers for graphs and hypergraphs. Recent work by Khanna, Putterman, and Sudan [SODA 2024] demonstrated near-linear sized \emph{combinatorial sparsifiers} for a broad class of CSPs, which they term \emph{field-affine CSPs}. Our main result is a polynomial-time algorithm that constructs a spectral CSP sparsifier of near-quadratic size for all field-affine CSPs. This class of CSPs includes graph (and hypergraph) cuts, XORs, and more generally, any predicate which can be written as $P(x_1, \dots x_r) = \mathbf{1}[\sum a_i x_i \neq b \mod p]$. Based on our notion of the spectral energy of a fractional assignment, we also define an analog of the second eigenvalue of a CSP instance. We then show an extension of Cheeger's inequality for all even-arity XOR CSPs, showing that this second eigenvalue loosely captures the ``expansion'' of the underlying CSP. This extension specializes to the case of Cheeger's inequality when all constraints are even XORs and thus gives a new generalization of this powerful inequality which converts the combinatorial notion of expansion to an analytic property.