Transcription factors (TFs) are the main regulators of gene expression, controlling diverse cellular processes such as development, differentiation, and disease progression. A comprehensive analysis of their interactomes and targetomes provides valuable insights into their functions, regulatory mechanisms, and context-dependent roles. This chapter presents a robust methodological framework for investigating the interactome and targetome of TFs, applicable to a wide range of TF families. This workflow integrates advanced proteomic approaches—affinity purification mass spectrometry (AP-MS) and proximity-dependent biotinylation (BioID)—with the cistromic method, chromatin immunoprecipitation sequencing (ChIP-Seq), to identify both stable and transient protein–protein interactions (PPIs) and to identify interactions with DNA (e.g., DNA-binding targets of TFs). The workflow involves the generation of inducible cell lines expressing each TF under study and performing three parallel proteocistromic experiments (AP-MS, BioID, and ChIP-Seq) along with data analysis for network visualization and functional annotation. The workflow is adaptable to various TF families and experimental contexts, offering a versatile platform for uncovering the dynamic regulatory networks that TFs mediate, on both medium and large scales. This workflow advances our ability to comprehensively characterize TF functions, facilitating a deeper understanding of gene regulation and its implications in both health and disease.