The planets’ gravitational interaction causes rhythmic changes in Earth’s orbital parameters (also called Milanković cycles), which have powerful applications in geology and astrochronology. For instance, the primary astronomical eccentricity cycle due to the secular frequency term (g
2−g
5) (∼405 kyr in the recent past) utilized in deep-time analyses is dominated by the orbits of Venus and Jupiter, i.e., long eccentricity cycle. The widely accepted and long-held view is that (g
2−g
5) was practically stable in the past and may hence be used as a “metronome” to reconstruct accurate geologic ages and chronologies. However, using state-of-the-art integrations of the solar system, we show here that (g
2−g
5) can become unstable over long timescales, without major changes in, or destabilization of, planetary orbits. The (g
2−g
5) disruption is due to the secular resonance σ
12 = (g
1 − g
2) + (s
1 − s
2), a major contributor to solar system chaos. We demonstrate that entering/exiting the σ
12 resonance is a common phenomenon on long timescales, occurring in ∼40% of our solutions. During σ
12-resonance episodes, (g
2−g
5) is very weak or absent and Earth’s orbital eccentricity and climate-forcing spectrum are unrecognizable compared to the recent past. Our results have fundamental implications for geology and astrochronology, as well as climate forcing, because the paradigm that the long eccentricity cycle is stable, dominates Earth's orbital eccentricity spectrum, and has a period of ∼405 kyr requires revision.