Land cover maps play an integral role in environmental management. However, countries and institutes encounter many challenges with producing timely, efficient, and temporally harmonized updates to their land cover maps. To address these issues we present a modular Regional Land Cover Monitoring System (RLCMS) architecture that is easily customized to create land cover products using primitive map layers. Primitive map layers are a suite of biophysical and end member maps, with land cover primitives representing the raw information needed to make decisions in a dichotomous key for land cover classification. We present best practices to create and assemble primitives from optical satellite using computing technologies, decision tree logic and Monte Carlo simulations to integrate their uncertainties. The concept is presented in the context of a regional land cover map based on a shared regional typology with 18 land cover classes agreed on by stakeholders from Cambodia, Laos PDR, Myanmar, Thailand, and Vietnam. We created annual map and uncertainty layers for the period 2000–2017. We found an overall accuracy of 94% when taking uncertainties into account. RLCMS produces consistent time series products using free long term historical Landsat and MODIS data. The customizable architecture can include a variety of sensors and machine learning algorithms to create primitives and the best suited smoothing can be applied on a primitive level. The system is transferable to all regions around the globe because of its use of publicly available global data (Landsat and MODIS) and easily adaptable architecture that allows for the incorporation of a customizable assembly logic to map different land cover typologies based on the user’s landscape monitoring objectives.