Ripe and pre-ripe harvesting are agricultural practices with significant consequences on fruit quality. Moreover, the synthesis and accumulation of several health-promoting bioactive compounds in fleshy fruits are highly influenced by the light quality and intensity as ripening progresses. During fruit ripening, phytochromes (Phys) and their associated signaling networks are crucial in connecting light stimuli perception and the accumulation of carotenoids, tocopherols and other antioxidants. In tomato (Solanum lycopersicum), a model species for climacteric fruit ripening, the Tyr252-to-His substitution in the conserved GAF domain of PHYTOCHROME 2 (SlPhyB2), known as the SlYHB2 allele, confers light-independent activation. Here, we explore the fruit-specific overexpression of native SlPhyB2 or its constitutively active allele SlYHB2 as a means to circumvent tomato fruit quality penalties associated with off-vine ripening under dark conditions. Our findings reveal that fruit-specific overexpression of either SlPhyB2 or SlYHB2 allele delays on-vine ripening, but only SlYHB2-overexpressing fruits can sustain high carotenoid and tocopherol synthesis when fruits are ripened off-vine under complete darkness. Accordingly, SlYHB2-overexpressing fruits exhibited more extensive increments in transcript abundance of genes associated with isoprenoid metabolism during off-vine ripening than fruits overexpressing the native SlPhyB2 allele. These findings demonstrate that mutation-based adjustments in PHY properties can significantly minimize penalties in carotenoid and tocopherol accumulation in tomato fruits due to suboptimal harvesting and storage conditions.