Cell fate maintenance is crucial to complete cell differentiation programs in view to obtain functional cells and tissue. Tomato mesocarp cells are normally committed too enlarge by the accumulation of water, sugar and organic acids characteristic of fleshy fruits. Program of mesocarp cell expansion also involved endoreduplication described as a strategy for rapid growth, giving the potential for maximum cell expansion. We previously identified a tomato EMS mutant altered for mesocarp cell size and ploidy level affecting the overall tissue morphology. We identified through mapping-by-sequencing the causal mutation in a gene coding for the first Guanylate Binding protein described in plants. Cellular, metabolomic and transcriptomic analyses indicated that disruption of SlGBP1 gene induced early termination of endoreduplication followed by resume of division at late stages of fruit growth. The study indicated that SlGBP1 is sufficient to repress polyploid divisions by maintaining the differentiation program of mesocarp cells.