We report results of a 9-year monitoring program that took place from 2001 to 2009 of the helium and carbon isotope (³He/⁴He, δ¹³C) and relative abundances ratios (CO₂/³He) of fumarole sites at Poás and Turrialba volcanoes, Costa Rica. Over the monitoring period, helium isotopes (³He/⁴He), δ¹³C_(CO2) and CO₂/³He values varied between 6.7-7.6 R_A (where R_A = 1.4 × 10^-6), -5.5 to -1.3‰ (vs. PDB) and 8.2-59.5 (×10⁹), respectively, at Poás Volcano. Corresponding values for Turrialba Volcano were 6.9-8.0 R_A, -4.4 to -2.7‰ and 9.4-19.6 (×10⁹), respectively. Notably, fumarole sites at both volcanoes underwent changes in temperature, intensity and areal extent during the 9-year period, and Poás Volcano experienced hydrophreatic eruptions and structural damage induced by a nearby earthquake. At both volcanoes, there were significant and sympathetic temporal changes involving all three geochemical parameters—notably in 2001 and 2006 at Poás and in 2001 and between 2005-2007 at Turrialba. We dismiss increased hydrothermal interaction, magma degassing and calcite precipitation as likely causes of the observed variations. Instead, by ascribing endmember compositions to the three principal contributors to the CO₂ inventory—mantle wedge as well as limestone and organic (sedimentary) carbon (both slab and crust derived)—we show that changes in observed He-CO₂ relationships mainly reflect enhanced crustal contributions of CO₂ and increased inputs from magma degassing. Such changes in the relative roles of crust and magma as suppliers of CO₂ are readily apparent in the He-CO₂ temporal record. This work supports calls for long-term geochemical monitoring to be included within hazard assessment and mitigation studies at active volcanoes.