To prepare cream cheese mixture by adding all ingredients to a bowl. Mix until smoot. At first it's going to feel like it's split and will never come together but keep at it!
Preheat a fan-forced oven to 180C (356F) or 160C (320F) for a fan forced oven. Line a cupcake tin with cupcake liners.
In the bowl of a stand mixer fitted with the paddle attachment, add the flour, baking powder, caster sugar and salt. Turn mixer on low speed and allow it to mix for a couple minutes to help everything combine well (alternatively you may do this by sifting the ingredients together). Add the softened butter and let it mix until it resembles a fine sand like texture.
Next, add milk, eggs, yogurt, oil, lemon and lime juice and vanilla extract in a large jug and whisk well.
Add wet ingredients to dry ingredients in a slow and steady stream until no dry ingredients are visible. Scrape down the bowl, add zest and mix for another 20 seconds.
Fill each cupcake liner 3/4 of the way (using an ice cream scoop to transfer the batter into the cupcake liners makes this a quick and easy process otherwise you can use two tablespoons). Scoop 1 teaspoon cheesecake mixture on top.
Bake for 20-25 min or until a toothpick inserted comes out clean. Allow them to cool completely on a wire cooling rack before frosting.
To prepare frosting add 1 teaspoon yellow food gel and 1 teaspoon green food gel to one half of the frosting along with some lime zest. This will be your lime cream cheese frosting. Add 1 teaspoon yellow food dye and 1 teaspoon lemon zest to the second half of the frosting.
Fit the end of a piping bag with a 1M tip and frost one swirl of green frosting. One swirl of yellow, followed by another green and finish with a small swirl of yellow on top. I've found the easiest way to do this is with two 1M piping tips and two separate bags. The tips cost about $3 each so they're quite cheap.