BBX proteins are B-Box zinc finger proteins that can act as transcription factors and regulators of protein complexes. Several BBX proteins play important roles in plant development. Two Arabidopsis thaliana microProteins belonging to the BBX family, named miP1a and miP1b, homotypically interact with and modulate the activity of other BBX proteins, including CONSTANS (AtCO), which transcriptionally activates the florigen gene, FLOWERING LOCUS T (FT). In tomato, the closest homologs of miP1a and miP1b are the microProteins SlBBX16 and SlBBX17. To deepen our understanding of the role of tomato microProteins in flowering, we constitutively expressed SlBBX16/17 in Arabidopsis and tomato (MicroTom) and examined possible interacting partners. Overexpression of the two tomato microProteins in Arabidopsis caused a delay in the flowering transition; however, the effect was weaker than that observed in Arabidopsis plants overexpressing the native miP1a/b microProteins. In tomato, overexpression of SlBBX17 prolonged the flowering period; this effect was accompanied by downregulation of the flowering inhibitor Self Pruning. Yeast-Two Hybrid analysis did not show a direct interaction between SlBBX16 and SlBBX17 and AtCO and its closest homolog in tomato, SlCOL1. On the other hand, SlBBX16 and SlBBX17 were able to hetero-oligomerize with TCMP-2, a cystine-knot peptide involved in flowering pattern and fruit development in tomato. Increasing the expression of both tomato microProteins also caused alterations in fruit development: overexpression of SlBBX17 resulted in a diminished number and size of ripe fruits as compared to WT plants, while overexpression of SlBBX16 caused delayed fruit production up to the breaker stage. These effects were associated with changes in the expression of genes regulating gibberellin content.