Tomatoes are important in human nutrition, as they are a source of carotenoids and phenolic compounds. However, transformation processes may alter the nutritional value of foods, decreasing the concentration of health-promoting compounds. This work aimed to explore the effects of industrial transformation on processed tomatoes (crushed pulp, puree and paste), as well as the effect of the different pre-processing technologies, rather than different manufacturing sites, in producing tomato paste. Results demonstrate that phenolics profiling can distinguish between different processed products as well as different paste pre-treatments (namely cold, warm and hot break), even though the latter underwent a final thermal treatment at > 100 °C. Analogously, the different processing sites could be discriminated thanks to their characteristic phenolic fingerprint. The greatest differences identified were between conjugated forms of flavonoids, phenylpropanoids and lignans. The latter were the most labile phenolics, followed by flavonoids and then phenylpropanoids. Results provide evidence for the potential of phenolic fingerprint to support traceability of transformation processes and to investigate their effect on the nutritional value of processed tomatoes.