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Achieving net-zero emissions at the scale of subnational regions requires technology portfolios that are both economically robust and compatible with local acceptance constraints. This study assesses transition pathways for the Canton of Jura (population ~89,000) towards a CO₂-neutral energy system in 2050 using an adapted EnergyScope framework, including both a centralized representation and a district-resolved, self-consumption-oriented variant. Two policy-relevant stress tests are analysed: (i) phased constraints on wind and photovoltaic deployment, reflecting siting and political limits, and (ii) the trade-off between energy autonomy and total system cost under uncertainty in import–export prices. The cost-optimal net-zero configuration is dominated by wind and photovoltaics, with an optimum around ~300 MW wind and ~150–200 MW photovoltaics, meeting local demand while halving total system cost relative to the reference case. Imposing the current cantonal wind target (90 MW) increases total cost by ~25% and shifts the system towards substantially higher photovoltaic deployment (≈600 MW) and greater sensitivity to market-price assumptions. Autonomy constraints show an economic optimum at ~100% autonomy in the unconstrained case, shifting to ~120% under wind curtailment. Global sensitivity analysis identifies wind capital cost as the dominant driver of total cost, followed by wind maintenance, heat pumps, and high-voltage photovoltaics.