Certain weeds can be used as cover species in bananas and coffee plantations. The objective of this study was to compare ground cover and abundance of weed species, between the organic and conventional production systems of banana and coffee. Selected farms under organic or conventional management located at Limón and Alajuela were surveyed for weeds, during 2015 and 2016. The minimum area methodology was used to determine sampling site size. At each sampling site, all weed species were identified and grouped into their respective taxonomic families. Percent soil cover by each species was also estimated by means of a visual scale. In both crops, weed diversity was higher when the herbicide glyphosate was used for weed control, although the ground cover for these species was kept at a minimum. These results are thought to arise from the fact that under the organic production system, a hierarchy of dominant species is established, which in turn inhibit many of the somewhat less adapted species, whereas under the conventional production system, the use of a non-residual herbicide renders the ground with plenty of space for species regeneration from the soil propagule bank. Organic weed management in both crops showed higher soil cover by weeds, but from a lower number of species. In contrast, chemical weed management with glyphosate showed a higher number at species, but a significant reduction in ground cover by those weeds.