We study the twisted index of 3d N = 2 supersymmetric gauge theories on S-1 x Sigma in the presence of a real FI parameter deformation. This parameter induces a 1d FI parameter for the effective supersymmetric quantum mechanics on S-1. Using supersymmetric localisation, the twisted index can be expressed as a contour integral. We show that the contour prescription is modified in the presence of the 1d FI parameter, leading to wall-crossing phenomena for the twisted index. In particular, we derive a general wall-crossing formula for abelian gauge theories. We also examine the origin of wall-crossing as change of stability condition in the algebro-geometric interpretation of the twisted index. These ideas are illustrated for abelian theories with N = 4 supersymmetry and in a non-abelian example that reproduces wall-crossing phenomena associated to moduli spaces of stable pairs.