Natural forest regeneration can be a slow and difficult-to-predict process because it is the result of complex interactions between seedling establishment success and site factors. Here, we applied a novel “lifetime” modelling approach to account for seed emergence and seedling survival across site conditions (i.e., seed protection and canopy cover) for Pinus nigra Arn. ssp. salzmannii—a forest type classified as a “habitat of interest” by the European Union. Lifetime analysis permits for simultaneous assessment of various binary “life” events since sowing, like seed emergence (or not) and seedling survival (or mortality). Modelling results showed that (i) seedling–tree interactions can vary depending on degree of canopy cover and (ii) climatic conditions of the sowing year can modulate the influence of shading (i.e., canopy cover) and predation over seed emergence and seedling survival. Outputs compared favourably to data collected during two, discrete, first-year growing seasons at typical montane Spanish black pine sites (in Serranía de Cuenca, Central-eastern Spain). To our knowledge, this is the first application of lifetime modelling to test multiple, coupled interactions on seedling emergence to inform regeneration biology for any forest tree species. Thus, these methods may be applied to inform management planning strategies for various forests (not just Spanish black pine) in the context of climate change