Health-beneficial properties of many secondary plant metabolites have created much interest into the control of their biosynthesis in crop species. Phenolic compounds, including flavonoids, hydroxycinnamates, and tannins, make up an important group of such phytonutrients. They are formed via the phenylpropanoid pathway and share common precursors with lignin, an insoluble cell wall-associated polymer. In this study, the aim was to reduce lignin biosynthesis so as to enhance the availability of these precursors and, thereby, stimulate the production of soluble, potentially health-promoting, phenolic compounds in tomato (Solanum lycopersicum L.). First two tomato genes encoding cinnamoyl-CoA reductase (CCR), a key enzyme in the formation of lignin monomers, were identified and characterized. Transgenic plants exhibiting a reduced lignin content were subsequently obtained through an RNAi strategy targeting one of these genes. As anticipated, the total level of soluble phenolics was higher in stems and leaves of the transformants as compared with control plants. This was correlated with an increased antioxidant capacity of the corresponding plant extracts. Analysis of the soluble phenolic fraction by HPLC-MS revealed that vegetative organs of CCR down-regulated plants contained higher amounts of chlorogenic acid and rutin, and accumulated new metabolites undetectable in the wild type, such as N-caffeoyl putrescine and kaempferol rutinoside. In fruits, CCR down-regulation triggered the moderate accumulation of two new compounds in the flesh, but the total phenolic content was not affected. Although the prospects of exploiting such a strategy for crop improvement are limited, the results provide further insight into the control of the phenylpropanoid pathway in the Solanaceae.