Field mapping is one of the most important aspects of precision agriculture, and community drones will be able to empower young rural entrepreneurs who will be the generational replacement of a new agrosocial paradigm. This research presents an agroecological participatory innovation methodology that utilizes precision technology through geographic information systems and unmanned aerial vehicles to evaluate the integrated ecological management of weeds for glyphosate substitution in a transitional area of Citrus sinensis in San Luis Potosí, Mexico. Modeling methods and spatial analyses supported by intelligent georeference protocols were used to determine the number of weeds with tolerance and glyphosate resistance. Four control flights were conducted to monitor seven treatments. Glyphosate-resistant weeds were represented with the highest number of individuals and frequency in all experimental treatments. Although the treatment with maize stubble showed a slightly better result than the use of Mucuna pruriens mulch, which prevents the emergence of glyphosate resistant weeds before emergence, the second treatment is considered better in terms of the cost–benefit ratio, not only because of significantly lower cost but also because of the additional benefits it offers. Geospatial technologies will determine the nature of citrus and fruit tree agroecological treatments and highlight areas of the plot with binomial soil and plant nutrient deficiencies and pest and disease infestations, which will improve the timely application of bio-inputs through the development of accurate maps of agroecological transitions.