Andean tropical glaciers have shown a clear shrinkage throughout the last few decades. However, it is unclear how this general retreat is associated with variations in rainfall patterns in the Amazon basin. To investigate this question, we compared the annual net accumulation variations in the Bolivian Cordillera Real (Andes), which is derived from an ice core from the Nevado Illimani (16° 37′ S, 67° 46′ W), covering the period 1960–1999 using the Amazonian Rainfall Index, Northern Atlantic Index (TNA), Multivariate ENSO Index (MEI), and Pacific Decadal Oscillation (PDO). The accumulation rate at the Nevado Illimani ice core decreased by almost 25% after 1980, from 1.02 w.eq. a−1 (water equivalent per year) in the 1961–1981 period to 0.76 w.eq. a−1 in the 1981–1999 period. The Northern Amazonian Rainfall (NAR) index best reflects changes in accumulation rates in the Bolivian ice core. Our proposal is based on two observations: (1) This area shows reduced rainfall associated with a more frequent and intense El Niño (during the positive phase of the MEI). The opposite (more rain) is true during La Niña phases. (2) Comparisons of the ice core record and NAR, PDO, and MEI indexes showed similar trends for the early 1980s, represented by a decrease in the accumulation rates and its standard deviations, probably indicating the same causality. The general changes observed by early 1980s coincided with the beginning of a PDO warm phase. This was followed by an increase in the Amazonian and tropical Andean precipitation from 1999, coinciding with a new PDO phase. However, this increase did not result in an expansion of the Zongo Glacier area.