Breeding resistance to whitefly-transmitted begomoviruses is an important goal of tomato breeding programmes worldwide. So far, resistance to begomoviruses in tomato has been achieved using wild species, and at least five resistance genes (Ty genes) have been studied. The present study was undertaken to combine Ty-2 and Ty-3 and to determine the effect of pyramiding on infection of tomato by three diverse begomovirus species. The diagnostic ability of the markers linked to Ty genes was assessed and marker-assisted selection was used to develop pyramided tomato lines from the crosses between Ty stocks. Five stable pyramided tomato lines that differ in fruit morphology and yield potential were developed. The horticultural performance of pyramided lines in field trials showed that the yield and horticultural traits are well maintained in the plants. The response of these lines was assessed using agroinoculation and field tests in a disease hotspot. The pyramided lines and Ty-3-carrying lines exhibited a high level of resistance to the monopartite and two bipartite begomoviruses tested. The pyramided tomato lines developed in this study could be important genetic resources for sustainable tomato production in areas affected by tomato leaf curl virus disease. The combined results of disease resistance tests also showed that Ty-3 is critical for achieving broad-spectrum resistance. The limitations of relying on a single gene and the importance of pyramiding are discussed in the light of available evidence on frequent recombination in begomoviruses.