This paper investigates the methodological and data challenges faced when conducting environmental life cycle assessments (LCAs) of alternative protein products. Drawing on interviews with 21 expert practitioners and a synthesis of recent LCA research, it identifies two overarching themes: the lack of clear best practices for methodological decision-making—particularly in designing functional units and allocation methods for novel food processes—and the prevalence of critical data gaps, which often force practitioners to use proxy data or assumptions that introduce significant uncertainty into results. The study details how these issues impact the credibility, comparability, and reliability of LCA results, especially for emerging plant-based, precision fermentation, and cultivated meat systems. It explores current efforts to integrate nutrition and broader impact categories into LCAs, analyzes the practical implications of various allocation approaches, and highlights the material effects of data limitations and methodological choices on reported outcomes. The paper concludes by recommending coordinated research, standardized data reporting, and methodological innovation to ensure LCAs remain a robust tool for sustainability assessment as the alternative protein sector evolves.