This study provides an empirical analysis of the impact of the disaster on technological innovation by employing the instrumental variable (2SLS) method and instrumental variable fixed-effect method in a panel of 45 African economies from 1990 to 2019. The empirical results confirm disaster’s negative and significant impact on innovation. A 1% increase in a disaster will lead to about − 13.750% decrease in scientific journals, − 3.302% decrease in R&D, and − 3.644% decrease in the TFP, respectively. These findings are supported by panel quantile regression. The study identifies four possible channels through which disaster lowers innovation in African economies: (i) reducing trade, (ii) total investment opportunities, and (iii) human capital. Various robustness tests support our findings. Finally, the study bolsters historical capital models for the adoption of cutting-edge technology in the building, provides critical policy recommendations on environmental laws, and advocates for disaster-response policies; decentralization of the energy industry away from disaster-affected areas for greater private sector participation; financial incentives for start-ups to facilitate trade and investment; creating a culture of prevention, preparation, and resilience at all levels via knowledge and innovation; and reconstruction as a method of establishing disaster-resistant structures and habitat to offer a safer living environment.