Combine flour, sugar, lime zest, cinnamon, nutmeg, and salt in a large bowl.
Fit pie crust in a 9-inch pie plate. Arrange guava slices on the bottom of the prepared pie crust, mounding slices of guava in the center of the crust. Sprinkle guavas with flour and sugar mixture. Drizzle pie filling with lime juice and dot with butter pieces.
Cover pie filling with the second pie crust and crimp the edges together. Make several slits in the top crust to allow the steam to escape.
Bake the pie in the preheated oven for 10 minutes. Reduce temperature to 350 degrees (175 degrees C) and bake until the filling is tender and the crust is golden, 30 to 40 minutes.