Cryptolepis sanguinolenta (Lindl.) Schlt., the main source of cryptolepine alkaloid, is intensively exploited in the wild to treat malaria and Lyme disease. In this study, the influence of four inorganic fertilizers (supplying N, P, K, or NPK) and four growth periods (3, 6, 9, and 12 months after transplanting) on the herb’s root biomass, cryptolepine content and yield, and biological activities were investigated in a pot and field trial. The results showed the application of N (in the form of Urea or NPK) increased root biomass yield, cryptolepine content, and cryptolepine yield compared to unfertilized plants. The 9-month-old plants recorded the maximum cryptolepine content (2.26 mg/100 mg dry root) and cryptolepine yield (304.08 mg/plant), indicating the perfect time to harvest the herb. Plant age at harvest had a more significant influence (50.6–55.7%) on cryptolepine production than fertilizer application (29.2–33.3%). Cryptolepine extracts from 9- to 12-month-old plants had the highest antiplasmodial activity (IC50 = 2.56–4.65 µg/mL) and drug selectivity index (2.15–3.91) against Plasmodium falciparum Dd2. These extracts were also cytotoxic to Jurkat leukaemia cell lines (CC50 < 62.56 µg/mL), indicating the possible use of cryptolepine for cancer management. Growing the herb in the field increased cryptolepine yield 2.5 times compared to growth in a pot, but this did not influence the antiplasmodial activity of the extract. Commercial cultivation of C. sanguinolenta for 9 months combined with N application could be a promising solution to the sustainable use of this threatened medicinal species.