Interrogating the stacking of two-dimensional polymers (2DPs) as a function of chemical composition is important to leverage their properties. We explore the dependence of 2DP crystallinity and porosity on variable amounts of zwitterions contained within the pores and find that high zwitterion loadings consistently diminish 2DP materials quality. A competition between disruptive zwitterion electrostatic forces and alkyl stabilization directs the stacking order of each 2DP and demonstrates the contrasting effects of side chain composition on 2DP crystallinity and porosity.