Reconstructing past climate conditions in boreal ecosystems remains a complex challenge due to the intricate interactions between both external and internal forcings, ecological dynamics, and methodological constraints. In this study, we present pollen- and chironomid-based temperature reconstructions from five boreal forest sites in eastern Canada, assessing their sensitivities, limitations, and potential for improving paleoclimatic interpretations. By applying multiple inference techniques and evaluating their reliability through statistical indices, we identify key internal factors that influence reconstruction accuracy. Our findings reveal that pollen-based temperature estimates are affected by multiple biases, including the impact of forest fires on vegetation dynamics, postglacial migration lags, and uncertainties in the temperature optima of overrepresented taxa. These biases vary considerably across different vegetation zones. Chironomid-based reconstructions, in contrast, generally exhibit stronger alignment with regional climate trends, but may be sensitive to local, lake-specific conditions. Integrating these insights, we refine the Holocene climatic history of eastern Canada, reconciling discrepancies with previous studies and producing more robust estimates of temperature variations during key climatic intervals, including the deglaciation, the Holocene Thermal Maximum, and the Neoglacial Period. These results enhance our understanding of past climate variability in boreal environments and provide a critical foundation for assessing future ecological responses to ongoing climate change.