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Phytoliths are essential palaeoecological proxies that play an immensely important role in palaeoclimatic studies. Their inert composition and general hardiness allow phytoliths to be preserved in geological settings, even when other plant fossils perish. This partially explains their utility for investigating plant communities and plant-human interactions on short and long timescales. Phytoliths also happen to be the most reliable source of fossil evidence for tracking the evolutionary history of grasses, arguably among the most crucial extant plant families. In the last two decades, the number of studies and publications in all fields of phytolith analysis has grown exponentially, mainly due to a diversification of research topics. Although significant progress has been made in applying phytolith analysis to answer archaeological, palaeoenvironmental, palaeoclimatological, evolutionary, and taxonomic questions, phytolith assemblages can be subject to pre- and post-depositional processes that might affect their preservation and thus could bias interpretation. This article reviews the importance of phytolith research in palaeoecology, discusses the constraints and taphonomic processes affecting phytolith analysis, and highlights the challenges in phytolith studies across various sediments. It emphasizes the significance of identifying phytolith transportation modes and understanding the impacts of taphonomic processes. Specific sampling strategies, such as targeting environments protected from surface weather conditions and selecting sediments with lower translocation rates or little horizon development, are suggested to preserve a diverse range of phytolith morphotypes. Caves and deltas are proposed as suitable alternatives to neritic marine sediments and carbonate-rich sites. This review also emphasizes the importance of sediment analysis, including grain size, sediment transport trend analysis, and micromorphology, complemented by analytical techniques and multi-proxy approaches. The inclusion of thin section studies, micromorphology, SEM, EDS, FT-IR, XRD, AAS/AES, XRF, and ICP-MS/AES is recommended to minimize depositional biases and help understand biases related to phytolith formation. Using mathematical models and correlation measurements to assess the impact of taphonomy on phytolith assemblages is also valuable. To conclude, we discuss some analytical considerations and suggest a methodological framework that integrates phytolith analysis with a sedimentological perspective. This approach aims to minimize the biases in phytolith analysis and enhance our understanding of palaeoecology. [ABSTRACT FROM AUTHOR]