Ecosystems are often indirectly connected through consumers with complex life cycles (CLC), in which different life stages inhabit different ecosystems. Using a structured consumer resource model that accounts for the independent effects of two resources on consumer growth and reproductive rates, we show that such indirect connections between ecosystems can result in alternative stable states characterized by adult-dominated and juvenile-dominated consumer populations. As a consequence, gradual changes in ecosystem productivity or mortality rates of the consumer can lead to dramatic and abrupt regime shifts across different ecosystems, hysteresis and counterintuitive changes in the consumer abundances. Whether these counter intuitive or abrupt responses occur depend on the relative productivity of both habitats and which consumer life-stage inhabits the manipulated ecosystem. These results demonstrate the strong yet complex interactions between ecosystems coupled through consumers with CLC and the need to think across ecosystems to reliably predict the consequences of natural or anthropogenic changes.