The management of production system regarding the sustainable use of medicinal plants rely, in part, on the operational approaches employed by actors in input-process-output (IPO) schemes. This is done in a bid to gain competitive performance in medicinal plants systems—both extractive (forest gathering) and cultivation (forest farming and farm plantation). In the context of Indonesia, one of the key medicinal plants producing regions of the world, there is scanty empirical evidence regarding the knowledge of the transformations in medicinal plants'production. Through a sample of 150 households in Java, Indonesia, the study sought to: (i) analyze the financial performance of medicinal plants in extractive and cultivation-based systems, and (ii) explore the management practices linked to three production systems. By computing the investments and returns spent for five years (2014–2018) in the three systems, the paper reveals that forest gathering yields the highest net benefit per average household (USD 598/year), as opposed to forest farming with the lowest net benefit (USD 7/year). On a production area basis, forest farming recorded the highest net benefit (USD 59/ha/year) while forest gathering has the lowest (USD 18/ha/year). Conversely, the highest brut return to family labor is achieved in forest gathering (USD 7.81/person-day) and the lowest in forest farming (USD 3.42/person-day). While forest gathering is presently well performing, its role as a provider of specific plant species which are not found in other production systems, signals pressure for this system. Management guidelines are needed to regulate this system and to assure its long-term complementary function. Future research on (i) the contribution of medicinal plants production systems to local livelihoods, and (ii) the sustainability of the medicinal plants management system, are required.