In a bowl, mix together flour, almond meal, baking powder, and salt. Set aside.
Add the sugar, eggs, and lemon zest to the bowl of an electric mixer.
Beat the eggs on medium to medium high speed until they are pale and fluffy.
Add the milk and olive oil.
Add the flour mixture and thyme. Mix until just combined.
Line a 12-muffin pan with paper liners. Fill about 2/3 of the way. Sprinkle with a few thyme leaves for decoration.
Bake in a preheated 350 degree oven for 18 to 22 minutes. Cool completely on a rack.
Make the honey cream by whipping the heavy cream with a mixer until the cream begins to thicken. Add the lemon juice, honey (to taste), and vanilla. Continue to beat until soft peaks form.
I cut my cupcakes in half, and filled them with cream. Like a little cake sandwich.