Since industrialization began, atmospheric CO2 (CO2) has increased from 270 to 415 ppm and is projected to reach 800-1000 ppm this century. Some Arabidopsis thaliana (Arabidopsis) genotypes delayed flowering in elevated CO2 relative to current CO2, while others showed no change or accelerations. To predict genotype-specific flowering behaviors, we must understand the mechanisms driving flowering response to rising CO2. CO2 changes alter photosynthesis and carbohydrates in plants. Plants sense carbohydrate levels, and exogenous carbohydrate application influences flowering time and flowering transcript levels. We asked how organismal changes in carbohydrates and transcription correlate with changes in flowering time under elevated CO2. We used a genotype (SG) of Arabidopsis that was selected for high fitness at elevated CO2 (700 ppm). SG delays flowering under elevated CO2 (700 ppm) relative to current CO2 (400 ppm). We compared SG to a closely related control genotype (CG) that shows no CO2-induced flowering change. We compared metabolomic and transcriptomic profiles in these genotypes at current and elevated CO2 to assess correlations with flowering in these conditions. While both genotypes altered carbohydrates in response to elevated CO2, SG had higher levels of sucrose than CG and showed a stronger increase in glucose and fructose in elevated CO2. Both genotypes demonstrated transcriptional changes, with CG increasing genes related to fructose 1,6-bisphosphate breakdown, amino acid synthesis, and secondary metabolites; and SG decreasing genes related to starch and sugar metabolism, but increasing genes involved in oligosaccharide production and sugar modifications. Genes associated with flowering regulation within the photoperiod, vernalization, and meristem identity pathways were altered in these genotypes. Elevated CO2 may alter carbohydrates to influence transcription in both genotypes and delayed flowering in SG. Changes in the oligosaccharide pool may contribute to delayed flowering in SG. This work extends the literature exploring genotypic-specific flowering responses to elevated CO2.