Preheat the oven to 180 C /Gas 4. Grease two 12-hole cupcake tins or line cups with paper cases.
Combine flour, sugar, baking powder, salt, cinnamon, nutmeg and ginger in a large bowl. In a second bowl, whisk together pumpkin puree, soya milk, oil and agave nectar until evenly blended. Make a well in the flour mixture and pour in pumpkin mixture; stir just until combined. Fold in chocolate chips.
Spoon mixture into paper cupcake cases, filling each 3/4 full. Bake in the preheated oven until tops spring back when lightly pressed, 18 to 20 minutes.
Meanwhile, beat creamed coconut, vanilla extract and icing sugar together in a bowl until fluffy. Refrigerate until use.
Remove cupcakes from the oven and cool in the tins for 5 minutes. Transfer to a wire rack to cool completely, about 20 minutes.
Ice the cooled cupcakes with coconut icing and sprinkle desiccated coconut on top.