Here an integrated three-step microbiological Fr 13 risk assessment (Zou and Davey, 2016) is synthesised for the first time. It is applied to vulnerability to failure of a batch-continuous pasteurizer for raw milk containing viable Mycobacterium avium subsp. paratuberculosis (MAP) - a chronic enteric pathogen linked to Crohn's disease in humans. Pasteurization of raw milk is therefore globally important. The aim was to advance the Fr 13 risk framework to an integrated 3-step microbiological failure synthesis to study how naturally occurring fluctuations in processing can be transmitted and impact multi-step processes. The 3 steps of the pasteurizer are the heat-up of raw milk, holding for thermal inactivation of contaminant MAP, and; cool-down of the heat-treated milk. Overall pasteurizer failure is defined as unwanted survival of MAP following holding and is characterised by a risk factor (p(2)) for milk leaving this step. Realistic large-scale pasteurization is simulated using a refined Monte Carlo (with Latin Hypercube) sampling. Results show that for a (Regulatory) design reduction of log(10) = 5.5 (>99.999%) in viable MAP on a heat-up to 72 degrees C with 15 s holding, and a design safety margin of 2%, p(2) = 5.75%. This equates to up to 21 failures with unwanted MAP survival each year - averaged over an extended period of daily batch-continuous operations. We show these microbiological failures can be mitigated by installing precise safety-integrity-level (SIL) mass flow control on the input raw milk and by ensuring a holding time of >= 15 s. Results appear generalizable and therefore could be applied to a range of integrated 3-step microbiological processes. Findings will be of direct interest to risk analysts and milk processors and manufactures of equipment. The work is part of an investigation and development of Fr 13 as a new risk assessment and process design tool. Crown Copyright (C) 2017 Published by Elsevier Ltd. All rights reserved.