Transmission electron microscopy can resolve the atomic structure of materials with 0.5 angstrom resolution. High-resolution transmission electron microscopy (HRTEM) of soft materials, however, is limited by beam damage. We characterized damage in a series of conjugated polymers comprising poly(3-hexylthiophene-2,5-diyl) (P3HT), poly(3-dodecylthiophene-2,5-diyl) (P3DDT), and poly[(5,6-difluoro-2,1,3-benzothiadiazol-4,7-diyl)-alt-(3,3"'-di(2-octyldodecyl)-2,2';5',2 '';5 '',2 -quaterthiophene-5,5"'-diyl)] (PffBT4T-2OD) by monitoring the decay of electron diffraction peaks as a function of dose rate, beam blanking, and temperature. We also measured the decay of low-loss electron energy-loss spectra as a function of dose rate. These damage experiments suggest that the dominant mechanism of beam damage in conjugated polymers is the diffusion of a reacting species generated from ionization, likely of side chains. Elucidating a mechanistic description of radiation effects leads to imaging protocols that can minimize damage, which enables the direct imaging of 3.6 angstrom pi-pi stacking in a solution-processed conjugated polymer (PffBT4T-2OD), improving state-of-the-art resolution of this class of materials by an order of magnitude.