Abstract Equatorial plasma bubbles (EPBs) are ionospheric irregularities generated by Rayleigh–Taylor instability (RTI) that disrupt satellite communications. We quantify secular change of RTI growth rates and isolate underlying drivers using WACCM‐X simulations. Results reveal a significant increase in RTI growth rates at plasma bubble initiation altitudes, with greenhouse gas cooling as the dominant driver and geomagnetic field secular variation modulating trends by longitude. We identify reduced recombination damping, often overlooked, as a major contributor. In the American/western sector, magnetic field secular variation produces localized decreases in RTI growth rates for magnetic field lines with apex altitudes of ∼250–320 km but predominantly enhances RTI growth rates for field lines with higher apex altitudes. Note that EPBs are initiated at the bottom F2 region, regardless of apex altitudes of field lines. Overall, the equatorial ionosphere is becoming more susceptible to RTI and plasma bubble development through stronger forcing and weaker damping.