Producer cell lines are continuously optimised to meet rising biotherapeutic demand. Insights gained from host-cell omics, complementing conventional bioprocess monitoring, may enable predictable product quality and the identification of critical process parameters. A bioprocess-integrated multi-omics approach addressing multiple key challenges was designed and evaluated, enabling parallel investigation of the host-cell proteome, phosphoproteome, metabolome, and secretome. To demonstrate applicability, a fed-batch culture of the open-access NISTCHO reference cell line was examined for protein and phosphorylation dynamics post-feeding. Simultaneous monitoring of nutrient consumption, metabolic excretions, product titer, and antibody quality attributes was conducted. Additionally, an in-house R package was developed to streamline large-scale time-course data analysis, enabling comprehensive identification of dynamic features and clustering of temporal behaviour. This study profiles over 7000 proteins and 10000 phosphorylation sites in response to altered nutrient availability around feeding windows distinct to different phases of the bioprocess. Identified signatures span regulators of redox homeostasis and metabolism, include key glycosylation-related enzymes directly impacting product attributes, and pinpoint regulatory phosphorylation sites governing stress responses, demonstrating the capability of this approach for high-quality bioprocess reference data generation.