Warming-induced shrub expansion on Arctic tundra (Arctic greening) is thought to warm up permafrost by several degrees, as shrubs trap blowing snow and increase snowpack thermal insulation, limiting permafrost winter cooling and facilitating its thaw. At Bylot Island, (Canadian high Arctic, 73°N) we monitored permafrost temperature at nearby unmanipulated herb tundra and shrub tundra sites and unexpectedly observed that low shrubs cool permafrost by 1.21°C over the November-February period. This is despite a snowpack twice as insulating in shrubs. Using heat transfer models and finite-element simulations, we show that this winter cooling is caused by thermal bridging through frozen shrub branches. This effect largely compensates the warming effect induced by the more insulating snow in shrubs. The cooling is partly canceled in spring when shrub branches under snow absorb solar radiation and accelerate permafrost warming. The overall effect is expected to depend on snow and shrub characteristics and terrain aspect. These significant perturbations of the permafrost thermal regime by shrub branches should be considered in projections of permafrost thawing, nutrient recycling and greenhouse gas emissions.