PurposeThis paper aims to assess the impact of digital financial innovation on financial system development in Common Market for eastern and Southern Africa (COMESA). This paper evaluates the dynamic relationship between digital financial innovation measures and financial system development using time series data from COMESA countries for the period 1997–2019.Design/methodology/approachA dynamic autoregressive distributed lag model (ARDL) was adopted and the mean group (MG), pooled mean group (PMG) and dynamic fixed effect (DFE) of the model were estimated to evaluate the short- and long-run impact. In addition, the dynamic generalized method of moments (DGMM) was adopted for a robustness check. The Hausman test results show PMG to be the most consistent and efficient estimator, while the coefficient of lagged dependent variable of different GMM is less than the fixed effect coefficient, and, as such, suggests system GMM is the most suitable estimator. Data for the study were sourced from World Bank Development Indicator (WDI, 2020), World Governance Indicator (WGI, 2020) and World Bank Global Financial Development Database (GFD, 2020).FindingsThe result shows that digital financial innovation significantly impacts financial system development in the long run. As such, the evidence revealed that automated teller machines (ATMs), point of sale (POS), mobile payments (MP) and mobile banking are significant and contribute positively to financial system development in the long run, while mobile money (MM) and Internet banking (INB) are insignificant but exhibit positive and inverse relationship with financial development respectively. Further investigation revealed that institutional quality and a stable macroeconomic environment including their interactive term are significantly imperative in predicting financial system development in the COMESA region.Practical implicationsResearchers recommend a cohesive and conscious policy that would checkmate the divergence in the short run and suggest a common regional innovative financial strategy that could be pursued to incentivize technology transfer needed to promote financial system development in the long run. More so, plausible product and process innovations may be adapted to complement innovative institutions in the different components of the COMESA financial system.Social implicationsDigital financial innovation services if well managed increase the inherent benefits in financial system development.Originality/valueTo the best of the authors’ knowledge, this paper presents new background information on digital financial innovation that may stimulate the development of the financial system, particularly in the COMESA region. It also exposes the relevance of digital financial innovation, institutional quality and stable macroeconomic environment as well as their interactive effect on COMESA financial system development.