Protein biomarkers in human serum provide critical insights into various physiological conditions and diseases, enabling early diagnosis, prognosis, and personalized treatment. However, detecting low-abundance protein biomarkers is challenging due to the presence of highly abundant proteins that make up ∼99% of the plasma proteome. Here, we report the use of in situ metal-organic framework (MOF) growth in serum to effectively deplete highly abundant serum proteins for integrated proteomic analysis. Through biomolecule-mediated nucleation of a zeolitic imidazolate framework (ZIF-8), abundant plasma proteins are selectively encapsulated within ZIF-8 and removed from serum via centrifugation, leaving a depleted protein fraction in the supernatant. Bottom-up proteomics analysis confirmed significant depletion of the topmost abundant proteins, many at depletion levels exceeding 95%. Such depletion enabled the identification of 277 total proteins in the supernatant (uncaptured) fraction in a single-shot analysis, including 54 proteins that were only identified after depletion, 12 drug targets, and many potential disease biomarkers. Top-down proteomics characterization of the captured and uncaptured protein fractions at the proteoform-level confirmed this method is not biased toward any specific proteoform of individual proteins. These results demonstrate that in situ MOF growth can selectively and effectively deplete high-abundance proteins from serum in a simple, low cost, one-pot synthesis to enable integrated top-down and bottom-up proteomic analysis of serum protein biomarkers.