The present study addressed the need for furan mitigation measures at the level of food production, where the effects of extrinsic (process-related) and intrinsic (product-related) properties on furan formation in vegetable-based systems were investigated. For the first time in the literature, the effect of high-pressure high-temperature (HPHT) processing on the formation of furan was demonstrated. HPHT processing was proven to be an interesting alternative for furan reduction in vegetable-based systems, when aiming for sterilization intensities. Following HPHT treatment, the furan concentrations of a wide range of individual vegetable purées dropped to levels close to the analytical limits (1–2 ng/g purée). A higher processing cost might limit the use of HPHT processing to high-value added products, which means that for many other conduction-heated food products, conventional heating would remain the standard technology. As a first step towards control of furan formation in the latter products, a mixed model regression was used to identify the major precursors in vegetable-based systems. Significant correlations were observed for vitamin C and sugars, which were attributed to the efficiency of the conversion and high concentrations, respectively. Next to furan, the HPHT- and thermally treated purées were analyzed for 2- and 3-methylfuran, which are likely to undergo the same metabolic fate as furan. For most of the vegetables tested, the total amount of methylfuran found in the thermally treated purées could not be ignored. Similarly to furan, there was a clear reduction in the concentrations found in the HPHT-treated purées.