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Microbial contamination can compromise the efficacy and safety of pharmaceutical products.Microbial counting tests are used to assess the microbiological quality of non-sterile pharmaceutical products required by most pharmacopoeia compendiums. Despite this, measurement uncertainty assessment for microbial count tests is rarely considered, which can lead to false compliance/non-compliance decisions. In this work we evaluated the matrix effects on microbial counting tests and their top-down uncertainty assessment, and evaluated measurement uncertainty using the bottom-up approach, inaddition to estimating the consumer's or producer's risks due to measurement uncertainty. The combined and expanded uncertainties calculated using the top-down approach considered accuracy (recovery) and accuracy as the main components of uncertainty. The uncertainty component of accuracy was the most relevant in 59% of the samples studied, while accuracy was the main source of uncertainty in only 41% of the samples, being observed that the greater the interference of the matrix, the greater the uncertainty factor and, consequently, the greater the asymmetry for the interval around the measurement. From the bottom-up approach, three main sources of uncertainty were identified and quantified: dilution factor, platelet volume and plaque count. The contribution of these sources of uncertainty depends on the measured value of microbial load in pharmaceutical products, the contribution of the dilution factor and uncertainties of the plated volume increase with the increase in the measured value, while the contribution of plate counting decreases with the increase of the measured value.It was possible to assess the risk of false decisions due to measurement uncertainty by estimating consumer or producer risks. The risks were evaluated using the Monte Carlo method. Therefore, the relevance of measuring uncertainty assessment has been demonstrated to ensure the reliability of microbial count test results and to support decision-making when assessing non-sterile pharmaceutical conformity/non-compliance.