Rare earth element (REE) analyses are reported on glauconite-bearing phosphorites from northeastern Algeria. These rocks of Paleocene-Eocene age are located in the Eastern part of the Saharan Atlas, where two localities were investigated: the Djebel El Kouif in the north and the Kef Essenoun in the south. The latter belongs to the world-class Djebel Onk mining deposit. Petrographic examination indicates that phosphorite from the main layer of the Kef Essenoun deposit has a significant abundance in glauconite grains, while their occurrence in the Djebel El Kouif is restricted to the basal levels. In both deposits, glauconite grains are richer in REEs than other co-existing particles (pellets, coprolites, enameloid and dentine of marine fish teeth), but the glauconites of the Kef Essenoun deposit exhibit significantly higher REE concentration (min = 654 ppm, max = 1760 ppm, average = 1146 ppm) than those of Djebel El Kouif deposit (min = 543 ppm, max = 623 ppm, average = 584 ppm). The whole-rock REE concentrations also show substantial differences between the two deposits and the REE enrichment in the Kef Essenoun main sub-layer is more likely the result of the high glauconite content. PAAS normalized-REE patterns of the glauconite grains display similar patterns between the northern and southern localities with weak negative Ce anomalies and slight middle REE enrichments. On the other hand, the pellets and whole phosphorite grains from the northern deposit indicate a REE source from oxic-suboxic seawater, whereas those from the Kef Essenoun deposit exhibit slight middle REE enriched patterns with weak negative Ce anomaly suggesting a different environment of deposition (i.e. a tendency to reduced conditions). These geochemical results along with previous petrographic studies confirm the allochthonous character of the main phosphorite sub-layer in Kef Essenoun, where winnowing, transport and re-deposition of previously deposited phosphorites resulted in high accumulation and formation of glauconite grains. The glauconitization process of fecal pellets happened in two stages and was controlled by semi-confined micro-environments. This can explain the abundance of glauconite grains in the phosphorites from Kef Essenoun deposit and their restricted occurrence in the basal levels of the Djebel El Kouif outcrop. •Evidence of substantial REE enrichments in glauconite grains comparing to coexisting particles (∑REE > 1000 ppm).•Glauconite grains show high Ca, P, Fe, Al, K and Si contents indicating the glauconitization of preexisting pellets.•REE-signature of glauconite grains emphasizes their allochthonous character (remobilization and re-worked grains).•The higher REE content in whole rock of the southern phosphorites is linked to the abundance of glauconite grains.