Storage of medicinal plants may cause deterioration of the active principles with time, thus, reducing the efficacy of plants. Therefore, quantification of the active principle is essential before using the crude drug. Phyllanthus amarus (PA) contains lignans, namely, phyllanthin and hypophyllanthin, which shows anti-hepatotoxic activity. In this paper, we highlight the effect of storage conditions on the quantification of bioactive markers by high-performance liquid chromatography (HPLC) analysis in the crude plant material of PA. HPLC analysis of crude PA samples stored for certain period at long-term study (LS, 30 °C and 65% RH), accelerated study (AS, 40°C and 75% RH), and real-time study (RT) conditions was carried out using the LiChroCART Purospher® STAR RP-18 endcapped (250 × 4.6 mm, 5 μm) column along with a Purospher STAR RP 18e (4.0 × 4.0 mm, 5 μm) guard column using methanol:water (70:30) at a flow rate of 0.7 mL min −1 with ultraviolet (UV) detection at 220 nm. The HPLC study indicated that PA samples kept under LS condition are rich in lignan contents as compared to the samples stored under AS and RT study conditions. Therefore, PA should be used fresh to get maximum concentration of active lignans or it should be stored under LS conditions up to 6 months.