A free-form Sudoku puzzle is a square arrangement of m times m cells such that the cells are partitioned into m subsets (called blocks) of equal cardinality. The goal of the puzzle is to place integers 1,...,m in the cells such that the numbers in every row, column and block are distinct. Represent each cell by a vertex and add edges between two vertices exactly when the corresponding cells, according to the rules, must contain different numbers. This yields the associated free-form Sudoku graph. This article studies the eigenvalues of free-form Sudoku graphs, most notably integrality. Further, we analyze the evolution of eigenvalues and eigenspaces of such graphs when the associated puzzle is subjected to a "blow up" operation, scaling the cell grid including its block partition.