The expression of Wnt/β-catenin signaling target genes is regulated by nuclear translocation of β-catenin, mainly in complex with T-cell factor (TCF)/lymphoid enhancer binding factor (LEF) factors. LEF1, a member of the TCF/LEF family of transcription factors, holds significant importance in both normal developmental processes and various pathological conditions such as cancer. Our objective was to characterize the function of two LEF1 isoforms, namely full-length LEF1 and ΔN-LEF1, via detecting the proteins they interact with by using TurboID-based proximity labeling. Additionally, we aimed to map their binding profiles throughout the genome by using the CUT&RUN technique. This investigation was conducted in the context of differentiating mouse embryonic stem cells under two conditions: the presence of a GSK-3 inhibitor known as CHIR99021 (CHIR), which serves to mimic Wnt pathway activation, and the absence of Wnt pathway activation. In our TurboID data, we detected both well-established LEF1 interactors such as Wnt enhanceosome components and new isoform-specific interactors, such as NuRD complex proteins and the transcription factor, ZSCAN10, in the presence and absence of CHIR, respectively. Notably, the enrichment of RNA-binding proteins, chromatin modifiers, and numerous novel transient interactors such as ubiquitin ligases, deubiquitinases, kinases and phosphatases with FL-LEF1 in the presence of CHIR underscores the impact of Wnt/β-catenin signaling on modulating LEF1 function in an isoform-specific manner. The CUT&RUN data discovered the binding of LEF1 isoforms to the Lef1 gene and intriguingly revealed an unexpected interaction with Zscan10. Our findings reveal new insights into isoform-specific interactions and the underlying mechanisms through which LEF1 isoforms function in regulating gene expression and warrant further studies characterizing the function of other TCF/LEF isoforms in a similar fashion.