Carotenoid biosynthesis in plants includes a complex series of desaturation/isomerisation reactions, catalysed by four independent enzymes. In bacteria and fungi one desaturase/isomerase enzyme completes the same series of reactions. In the present study, a bacterial desaturase (crtI) from Pantoea ananatis has been overexpressed in the tangerine mutant of tomato (Solanum lycopersicon) which accumulates cis carotene isomers in the fruit due to a defective isomerase (CRTISO) and the old gold crimson (ogc) tomato mutant, which is defective in the fruit-enhanced lycopene β-cyclase (CYCB). Comprehensive molecular and biochemical characterisation of the resulting lines expressing crtI has revealed negative feedback mechanisms, acting predominantly at the level of phytoene synthase-1 (PSY1), and feed-forward mechanisms inducing cyclisation. In both cases, altered transcription appears to be the progenitor, with subsequent post-transcriptional modulation highlighting the complexity of the processes involved in modulating carotenoid homeostasis in plant tissues.