Abstract Habitat fragmentation is a critical threat to biodiversity, as it creates isolated patches of habitat and hinders species movement and survival. Systematic conservation planning (SCP) has advanced to include landscape connectivity, often using graph‐based models to assess and enhance habitat networks. We introduce GECOT, an open‐source command line tool for solving budget‐constrained multispecies landscape connectivity optimization problems when measuring landscape connectivity with the probability of connectivity (PC) indicator. GECOT builds on a theoretical framework to model conservation and restoration planning as a connectivity optimization problem where options impact the quantity or quality of available habitat and the permeability of habitat and landscape matrix. For a given case study, GECOT can be used to find the optimal solution using a mixed‐integer linear solver or heuristic solutions with different sub‐optimal algorithms when the optimal solution is too expensive in computation time.