Conservation agriculture (CA) is a sustainable management system that optimises yield while reducing input costs. However, reduction in tillage intensity and frequency as practised under CA generally alters weed densities and composition. The objective of the study was to evaluate the effect of tillage, cropping system and fertiliser rate on weed density and diversity under CA systems compared with conventional tillage (CT). An on-station field trial with a split-plot, randomised complete block design, was used and included two tillage systems, three cropping systems and two fertiliser levels. Reduced tillage had significantly (p < 0.05) higher weed density (42 m−2) but lower weed biomass (154 g m−2) in contrast to CT with lower weed density (36 m−2) and higher weed biomass (242 g m−2). In a principal component analysis ordination, Datura ferox and Tribulus terrestris were more strongly associated with high fertiliser rate, whereas Zinnia peruviana was associated with CT. The increase in weed density and diversity under reduced tillage is likely to restrain the adoption of CA. Therefore, there is a need for alternative weed management options depending upon the weed spectrum, cropping system and fertiliser management.