Palynological and archaeobotanical analyses were conducted on excavated sediments from Tse Dura, a Later Stone Age rock shelter in north-central Nigeria with the aim of reconstructing the environment conditions at the site within the last millennium. From 933 ± 29 BP to 802 ± 29 BP, the environment alternated between Guinea savanna with dry conditions, and secondary and riverine forests with humid conditions. During these periods of environmental fluctuations, the LSA populations engaged in the management of economic plants the most significant of which included Dioscorea spp. Pennisetum glaucum and Elaeis guineensis, and exploited wild plants such as Pavetta crassipes, Sarcocephalus latifolius and Lophira cf. lanceolata for dietary and ethnomedicinal purposes. Around 310 ± 30 BP cal, the environment became very wet after which it was succeeded by a drier period. It was during this period that Sorghum bicolor became prominent, and the environment attained its current status dominated by Guinea savanna elements and secondary forests.