Calcium phosphate is widely used for the remediation of lead-contaminated sites, where calcium/lead phosphate coprecipitates (Ca/Pb CoPs) form. This research investigated such coprecipitation with model low-molecular-weight organics (LMWOs), produced in the rhizosphere with representative functional groups, which were found to regulate both the composition (Ca/Pb and C/Pb ratios) and stability (aggregation and transformation) of Ca/Pb CoPs. The strong complexation ability of -SH in l-cysteine with aqueous Ca2+/Pb2+ ions inhibited coprecipitation to a great extent. Meanwhile, coprecipitates with lysine containing both -NH2 and -COOH had a higher Ca/Pb ratio than those with citrate containing only -COOH, probably due to the elevated local supersaturation caused by both -NH2 and -COOH in lysine that attracted phosphate ions and cations, promoting Ca doping in CoPs. Also, the strong binding of both -NH2 and -COOH with coprecipitates resulted in a higher C/Pb ratio for the CoPs with lysine than citrate. The oriented aggregation of nano-CoPs formed needle-shaped hydroxylpyromorphite crystals without organics. Unexpectedly, lysine/citrate disrupted and l-cysteine promoted such oriented aggregation, resulting in inhibited and promoted crystallinity, respectively. This study provided new mechanistic insights on LMWO effects on Ca/Pb CoP formation and their stability and can help understand Pb speciation and availability in the rhizosphere.