Speleothems from Ashalim Cave, located in the arid central Negev Desert, Israel, were used in a reconstruction of the palaeoclimate of the northern Saharan–Arabian desert margin. The sequence of speleothems is composed of three stratigraphic members: the yellow Pliocene Basal Member, the brown Early Pleistocene Intermediate Member and the thin Middle–Late Pleistocene Young Member. The age of the Basal Member is c. 3.1 Ma and the base of the Intermediate Member is 1.272 ± 0.018 Ma. Two last deposition periods of the Young Member occurred at 221–190 ka (Negev Humid Period (NHP) 2) and 134–114 ka (NHP-1), associated with interglacial marine isotopic stages 7.3–7.1 and 5.5, respectively. NHP-1 and -2 occurred when the African monsoon index was highest in the last 221 ka. The δ¹⁸O values of the speleothems range between −6.9 and −11.2‰, 2–4‰ less than in the speleothems of central and northern Israel. This may indicate a remote southern tropical source of precipitation, although during NHP-1 and -2 the thickness of the Negev Desert speleothems decreases from north to south, showing a stronger northern Mediterranean source of moisture. The δ¹³C values of the speleothems (3.5 to −8.5‰) show steppe to semi-desert C4 type vegetation. The ⁸⁷Sr/⁸⁶Sr ratios of the speleothems increased from c. 0.7078 in the Pliocene to 0.7082–0.7085 in the Pleistocene, indicating an increasing supply of desert dust and a decrease in host rock weathering.