Fruit carbonate of Buglossoides arvensis (syn. Lithospermum arvense) is a valuable dating and paleoenvironmental proxy for late Quaternary deposits and cultural layers because CaCO3 in fruit is assumed to be accumulated from photosynthetic carbon (C). However, considering the uptake of HCO3– by roots from soil solution, the estimated age could be too old depending on the source of HCO3– allocated in fruit carbonate. Until now, no studies have assessed the contributions of photosynthetic and soil C to the fruit carbonate. To evaluate this, the allocation of photo-assimilated carbon and root uptake of HCO3– was examined by radiocarbon (14C) labeling and tracing. B. arvensis was grown in carbonate-free and carbonate-containing soils (sand and loess, respectively), where 14C was provided as (1) 14CO2 in the atmosphere (5 times shoot pulse labeling), or (2) Na214CO3 in soil solution (root-labeling; 5 times by injecting labeled solution into the soil) during one month of fruit development. Distinctly different patterns of 14C distribution in plant organs after root- and shoot labeling showed the ability of B. arvensis to take up HCO3– from soil solution. The highest 14C activity from root labeling was recovered in roots, followed by shoots, fruit organics, and fruit carbonate. In contrast, 14C activity after shoot labeling was the highest in shoots, followed by fruit organics, roots and fruit carbonate. Total photo-assimilated C incorporated via shoot labeling in loess-grown plants was 1.51 mg lower than in sand, reflecting the presence of dissolved carbonate (i.e. CaCO3) in loess. Loess carbonate dissolution and root-respired CO2 in soil solution are both sources of HCO3– for root uptake. Considering this dilution effect by carbonates, the total incorporated HCO3– comprised 0.15% of C in fruit carbonate after 10 hr of shoot labeling. However, if the incorporated HCO3– during 10 hr of shoot labeling is extrapolated for the whole month of fruit development (i.e. 420-hr photoperiod), fruit carbonate in loess-grown plants incorporated approximately 6.3% more HCO3– than in sand. Therefore, fruit carbonates from plants grown on calcareous soils may yield overestimated 14C ages around 500 yr because of a few percentage uptake of HCO3– by roots. However, the age overestimation because of HCO3– uptake becomes insignificant in fruits older than approximately 11,000 yr due to increasing uncertainties in age determination.