Elemental fingerprinting could improve geographic origin authentication and quality control of tea. A comprehensive elemental fingerprinting method for ripen Pu-erh tea (RPT) using microwave digestion combined with inductively coupled plasma mass spectrometry (ICP-MS) has been developed, which enabled an accurate quantification of 69 elements. The developed method presented wide dynamic ranges (more than 3-order magnitude, R2 > 0.997), high sensitivity (LODs: 0.0001–8.105 μg/g, LOQs: 0.0003–27.015 μg/g), high accuracy (recoveries: 77.7%–118.2%) and repeatability (relative standard deviation: 0.6–18.8%). The effect of major geographical origins and the pile-fermentation process on the multi-element profiles of RPT was investigated by applying this method. 35 and 31 elements were significantly differential in Pu'er vs. Lincang region, and Pu'er vs. Xishuangbanna region (p < 0.05), respectively, and most of them presented lower levels in Pu'er region. Mo, Nd, Ce, Sr, Ba, V, and Tm were identified as the most relevant elements as potential discriminant indicators of different geographical origins. A prevailing elemental accumulation was revealed during pile-fermentation. 36 elements were significantly enriched in RPT after pile-fermentation. In particular, elements Ti, Cs, Nb, Eu, Zr, Tl, Cr, Co, Dy, Y and Si were most prominently enriched after pile-fermentation with folds changes of 1.55–2.02. This study is expected to provide comprehensive data for origin traceability of RPT, and advanced the understanding of the elemental enrichment mechanism during pile-fermentation of RPT.