Marine ecosystems are increasingly reshaped by climate change and human activities, resulting in novelty in species assemblages that have shifted beyond historical baselines. One unresolved question is how novelty influences resilience. Here, we examine how novelty arises in ecosystems when they transition through phases and affects resilience using the adaptive cycle framework. We use results from an ecosystem model of the Finnish Archipelago Sea (Baltic Sea) under contrasting climate, nutrient load and fishing scenarios. We quantify novelty in species composition and biomass and use ecological network analysis indices to identify adaptive cycle phases and resilience. Results suggest resilience decreases with higher novelty under warmer climate scenarios. Low nutrient load scenarios facilitate faster adaptive cycles and greater resilience than high nutrient load scenarios under the same climate conditions. Connecting network indices to the adaptive cycle helps to understand how the growing human-induced novelty influences resilience, supporting core resilience theory.