We consider N-fold 4-block decomposable integer programs, which simultaneously generalize N-fold integer programs and two-stage stochastic integer programs with N scenarios. In previous work [R. Hemmecke, M. Koeppe, R. Weismantel, A polynomial-time algorithm for optimizing over N-fold 4-block decomposable integer programs, Proc. IPCO 2010, Lecture Notes in Computer Science, vol. 6080, Springer, 2010, pp. 219–229], it was proved that for fixed blocks but variable N, these integer programs are polynomial-time solvable for any linear objective. We extend this result to the minimization of separable convex objective functions. Our algorithm combines Graver basis techniques with a proximity result [D.S. Hochbaum and J.G. Shanthikumar, Convex separable optimization is not much harder than linear optimization, J. ACM 37 (1990), 843–862], which allows us to use convex continuous optimization as a subroutine.