A free-form Sudoku puzzle is a square arrangement of m × 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.