Preheat the oven to 350°F (175°C). Line a 9x13-inch baking pan with foil and spray the foil with nonstick cooking spray.
In a large bowl, stir the melted butter with the granulated sugar and packed light brown sugar until combined.
Add the eggs one at a time, mixing fully after each addition, then mix in the vanilla, salt, and baking soda.
Slowly add the all-purpose flour and mix until just combined, then fold in the chocolate chips.
In a small bowl, stir the sweetened condensed milk with the creamy peanut butter until smooth.
Press about half of the cookie dough evenly into the prepared pan (spray hands with nonstick spray to prevent sticking).
Arrange the miniature peanut butter cups in a single layer over the bottom dough.
Carefully pour the sweetened condensed milk and peanut butter mixture over the peanut butter cups, leaving about a 1/4-inch gap at the edges so the mixture doesn't touch the foil.
Break the remaining cookie dough into pieces and distribute them over the condensed milk layer, pressing gently to flatten; it may not completely cover the layer.
Bake for 30–35 minutes, or until the tops of the bars just begin to turn golden brown.
Cool completely in the pan, then lift out using the foil and slice into bars.