Dataset Abstract: This dataset contains the raw and tidy experimental data underlying the study "Eco-evolutionary conflict: selfish adaptation undermines ecosystem persistence in microbial biospheres." The data was generated through a two-phase experimental design: (1) a long-term evolution experiment (246 days) of Escherichia coli strains (MC4100 and W) under resource-limited monoculture conditions, and (2) a subsequent co-culture biosphere experiment pairing evolved/wild-type E. coli with the alga Chlamydomonas reinhardtii in closed systems. The dataset includes the following components: Phenotypic Assay Data: Raw optical density (OD) measurements quantifying biofilm formation (Crystal Violet assay) and qualitative scoring of motility (Congo Red Agar and Tissue Culture Plate assays) for wild-type and evolved E. coli populations. Bacterial Growth Kinetics: Time-series OD600 measurements recording the growth of E. coli strains in LB broth and M9 minimal media supplemented with five different carbon sources (glucose, glycerol, gluconate, acetate, xylose). Data is arranged by time points and well coordinates, covering growth rate, carrying capacity, and area under the curve (AUC) assessments. Biosphere Fluorescence Monitoring: Long-term non-invasive chlorophyll fluorescence readings (RFU) serving as a proxy for C. reinhardtii photosynthetic activity in the co-cultured biospheres. This time-series data spans the full duration of the biosphere persistence experiment (84 days). Population Abundance Counts: Discrete cell count data obtained via flow cytometry (for C. reinhardtii, distinguishing total vs. fluorescent events) and Single Plate-Serial Spotting (SP-SDS) plating (for E. coli CFU/mL). Samples were destructively harvested and quantified at three key time points (Day 14, Day 43, and Day 84). Files are provided in standard .csv or .xlsx formats. Each file includes headers defining sample IDs (e.g., MWT, M1-M3, WWT, W1-W3), time points (days/hours), and measured variables (OD600, Fluorescence, Cells/mL). No significant data imputation was performed; missing values (if any) represent excluded technical replicates due to contamination or instrument error.