This data report presents the in-situ LA-ICP-MS trace element geochemistry of the micas of the Pan-African rare-element pegmatites of the Alto Ligonha Pegmatite District in northern Mozambique. The pegmatites contain Li-rich micas and primary Li aluminosilicates, such as spodumene. Five Alto Ligonha pegmatites, Naípa, Muiâne, Napepesso West, Nanro, and Natxepo, were investigated to better understand the fractionation of pegmatite melts leading to Li enrichment, utilizing e.g. the trace element chemistry of mica from different parts of these pegmatites. Micas collected from the wall zone, intermediate zone and core zone of the studied pegmatites show high but also highly variable concentrations of the incompatible elements like Li, Rb, Cs, Be, and Ta. Very strong pegmatite-internal fractionation is recorded by the mica chemistry of the Naípa, Muiâne and Nanro pegmatites. In these pegmatites, Li2O in white micas measured with LA-ICP-MS increases from 0.1-1.4 wt.% in the wall zone, to 0.3-1.7 wt.% in the intermediate zone, 1.5-3.8 wt.% in the core zone and up to 5.4 wt.% in the pockets. The data record extreme Li enrichment during the final crystallization stage.