Pseudosection modelling is rapidly becoming an essential part of a petrologist’s toolkit and often forms the basis of interpreting the tectonothermal evolution of a rock sample, outcrop, or geological region. Of the several factors that can affect the accuracy and precision of such calculated phase diagrams, “geological” uncertainty related to natural petrographic variation at the hand sample- and/or thin section-scale is rarely considered. Such uncertainty influences the sample’s bulk composition, which is the primary control on its equilibrium phase relationships and thus the interpreted pressure–temperature (P–T) conditions of formation. Two case study examples—a garnet–cordierite granofels and a garnet–staurolite–kyanite schist—are used to compare the relative importance that geological uncertainty has on bulk compositions determined via (1) X-ray fluorescence (XRF) or (2) point counting techniques. We show that only minor mineralogical variation at the thin-section scale propagates through the phase equilibria modelling procedure and affects the absolute P–T conditions at which key assemblages are stable. Absolute displacements of equilibria can approach ±1 kbar for only a moderate degree of modal proportion uncertainty, thus being essentially similar to the magnitudes reported for analytical uncertainties in conventional thermobarometry. Bulk compositions determined from multiple thin sections of a heterogeneous garnet–staurolite–kyanite schist show a wide range in major-element oxides, owing to notable variation in mineral proportions. Pseudosections constructed for individual point count-derived bulks accurately reproduce this variability on a case-by-case basis, though averaged proportions do not correlate with those calculated at equivalent peak P–T conditions for a whole-rock XRF-derived bulk composition. The main discrepancies relate to varying proportions of matrix phases (primarily mica) relative to porphyroblasts (primarily staurolite and kyanite), indicating that point counting preserves small-scale petrographic features that are otherwise averaged out in XRF analysis of a larger sample. Careful consideration of the size of the equilibration volume, the constituents that comprise the effective bulk composition, and the best technique to employ for its determination based on rock type and petrographic character, offer the best chance to produce trustworthy data from pseudosection analysis.