We construct the geometric Baum-Connes assembly map for twisted Lie groupoids, that means for Lie groupoids together with a given groupoid equivariant \(PU(H)-\)principle bundle. The construction is based on the use of geometric deformation groupoids, these objects allow in particular to give a geometric construction of the associated pushforward maps and to establish the functoriality. The main results in this paper are to define the geometric twisted K-homology groups and to construct the assembly map. Even in the untwisted case the fact that the geometric twisted K-homology groups and the geometric assembly map are well defined for Lie groupoids is new, as it was only sketched by Connes in his book for general Lie groupoids without any restrictive hypothesis, in particular for non Hausdorff Lie groupoids. We also prove the Morita invariance of the assembly map, giving thus a precise meaning to the geometric assembly map for twisted differentiable stacks. We discuss the relation of the assembly map with the associated assembly map of the \(S^1\)-central extension. The relation with the analytic assembly map is treated, as well as some cases in which we have an isomorphism. One important tool is the twisted Thom isomorphism in the groupoid equivariant case which we establish in the appendix.