Yes you can. When I was little, we did not have enough fresh vegetables in the winter, and in the summer/fall the families would grill peppers and eggplants, make the spreads and preserve them in the freezer for the use in the winter monts.
For Baba Ganoush, I roast the eggplant on a grill (charcoal just past its flaming and hottest point) first until it's blackened and shriveled (about 1 hour). Then I scoop out the insides and freeze those in freezer bags, 1 eggplant per bag. When I thaw it, I just drain out some of the extra liquid and blend up as usual for the Baba Ganoush. I've done it this way for years and it's always delicious, even 3-4 months later in the middle of winter.
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