You could, it depends on your recipe really. Mine relies on eggs to do the thickening, so I'd add in another large egg myself. It's really a variant of custard pie, and in most recipes that is the reason for the texture. Flour or cornstarch will thicken it of course, but they will also change the texture and the coloration of the jell. You might also want to increase the total baking time as well, not removing the pie until it barely jiggles in the middle. That might mean placing a foil shield over the top and edges, but would help the firmness of set.
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No, don’t add flour to make the pecan pie filling set…if will muddy the flavours of the nuts, sugar and butter.
Rather, cook it longer.
If you want more info, see the blue “millicanpecan.com” for more details about causes for a loose or unset filling and how to fix.