The formation of plant organs requires a cascade of regulatory processes which triggers gene expression, protein synthesis, and biochemical reactions that shape cellular structures and functions. Central to these processes are proteins, often transcription factors, which rarely work alone, but in cooperation with other proteins to form dynamic interactions to achieve a correct regulation. In this review, we explore the role of protein-protein interactions in flower and fruit development. For this, we start with transcription factors and how their functions are modulated through physical interactions with other proteins. We list a set of current techniques to study protein interactions in reproductive development, along with emerging methodologies. Additionally, we discuss key molecular mechanisms mediated by protein-protein interactions such as recognition specificity, DNA binding, and protein complex formation. Finally, we describe some current challenges and future directions in the study of flower development.