Cells constantly incur DNA damage arising from endogenous and exogenous sources. Homologous recombination (HR)-based DNA repair pathways drive restoration of damaged DNA to its original state. While HR is considered an error-free form of DNA repair, dysregulated HR can result in loss of heterozygosity (LOH) or gross chromosomal rearrangements (GCRs) that in multicellular eukaryotes can drive the onset of cancer. The PI3K-like kinase (PIKK) Mec1/ATR is a major regulator of DNA end resection that has been implicated in the regulation of homologous recombination, although the extent and mechanism of its involvement remains unclear. The lack of a detailed understanding of the full scope of Mec1/ATR substrates represents a major gap in our understanding of HR regulation. In this work I use quantitative phosphoproteomics to expand the Mec1/ATR substrate network and uncover molecular mechanisms by which Mec1/ATR promotes genome integrity via homologous recombination control. I reveal an interaction between the DNA repair helicase Sgs1 and the phospho-protein scaffold Dpb11 in S. cerevisiae that is critical for preventing nonallelic recombination. I then translate these findings to human cell lines to generate ATR substrate networks dependent on resection and DNA damage. These findings expand our understanding of the action of Mec1/ATR in genome maintenance and will inform strategies for exploiting synthetic genetic interactions to selectively kill cancer cells using ATR inhibitors currently in clinical trials.