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1. In biodiversity monitoring, large datasets are becoming more and more widely available and are increasingly used globally to estimate species trends and conservation status. These large-scale datasets challenge existing statistical analysis methods, many of which are not adapted to their size, incompleteness and heterogeneity. The development of scalable methods to impute missing data in incomplete large-scale monitoring datasets is crucial to balance sampling in time or space and thus better inform conservation policies. 2. We developed a new method based on penalized Poisson models to impute and analyse incomplete monitoring data in a large-scale framework. The method allows parameterization of (a) space and time factors, (b) the main effects of predictor covariates, as well as (c) space-time interactions. It also benefits from robust statistical and computational capability in large-scale settings.3. The method was tested extensively on both simulated and real-life waterbird data, with the findings revealing that it outperforms six existing methods in terms of missing data imputation errors. Applying the method to 16 waterbird species, we estimated their long-term trends for the first time at the entire North African scale, a region where monitoring data suffer from many gaps in space and time series.4. This new approach opens promising perspectives to increase the accuracy of species-abundance trend estimations. We made it freely available in the r package

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