PurposeThis work aims to analyse the relationship between public health efficiency and well-being considering a panel of 102 Italian provinces from 2000 to 2016 and evaluates if there are omitted variable biases and endogeneity biases and also evaluates if there are heterogeneous effects among provinces with different income levels.Design/methodology/approachWe use a multi-input and output bootstrap data envelopment analysis to assess public health efficiency. Then, we measure well-being indices using the min-max linear scaling transformation technique. A two-stage least squares model is used to identify the causal effect of improving public health efficiency on well-being to account for time-invariant heterogeneity, omitted variable bias and endogeneity bias.FindingsAfter controlling for important economic factors, the results show a significant effect of an accountable and efficient public health system on well-being. Those effects are concentrated in the North, the most economically, geographically and environmentally advantageous areas.Research limitations/implicationsThe use of the sample mean, probably the oldest and most used method for aggregating the indicators, could be affected by variable compensation, with consequent misleading results in the process of constructing the well-being index. Another limitation is the use of lagged values of the main predictor as an instrument in the instrumental variables setting because it could lead to information loss. Finally, the availability of data over a long period of time.Practical implicationsThe findings could help policymakers adopt measures to strengthen the public health system, encourage private providers and inspire countries worldwide.Social implicationsThese results draw the attention of local authorities, who play an important role in designing and implementing policies to stimulate local public health efficiency, which puts individuals in the conditions of achieving overall well-being in their communities.Originality/valueFor the first time in Italy, a panel of well-being indices was constructed by developing new methodologies based on microeconomic theory. Furthermore, for the first time, the assessment of the relationship between public health efficiency and well-being is carried out using a panel of 102 Italian provinces.