  In this paper we consider non-anticommutative field theories in $\mathcal{N}
=2$ superspace formalism on three-dimensional manifolds with a boundary. We
modify the original Lagrangian in such a way that it preserves half the
supersymmetry even in the presence of a boundary. We also analyse the partial
breaking of supersymmetry caused by non-anticommutativity between fermionic
coordinates. Unlike in four dimensions, in three dimensions a theory with
$\mathcal{N} =1/2$ supersymmetry cannot be obtained by a non-anticommutative
deformation of an $\mathcal{N} =1$ theory. However, in this paper we construct
a three dimensional theory with $\mathcal{N} =1/2$ supersymmetry by studying a
combination of non-anticommutativity and boundary effects, starting from
$\mathcal{N} =2$ supersymmetry.
