Transparent photovoltaics that harvest ultraviolet photons are promising point‐of‐use power sources for lower power applications, such as electrochromic windows that regulate the flow of visible and infrared photons for lighting and temperature regulation. Organic photovoltaic cells employing contorted hexabenzocoronene (cHBC) and its derivatives as chromophores have shown promise for transparent solar cells due to their high open‐circuit voltages, large‐area scalability, and high photoactive layer transparency. Here, the operational stability of such devices is investigated and it is found that the solar cell active layers that include peripherally halogenated chromophores undergo rapid morphological degradation during operation, while control cells employing cHBC and other non‐halogenated derivatives as donors with archetype C70 as an acceptor are highly stable. This study suggests halogenation of chromophores can play an outsized role in determining the operational stability of devices comprising them, which should be considered during the molecular design process.