Heat a large skillet; add the bacon and cook over moderate heat until crisp, about 4 minutes. Using a slotted spoon, transfer the bacon to paper towels to drain. Pour off all but 3 tablespoons of the fat from the skillet.
Add the onion to the skillet and cook over moderate heat until softened, about 3 minutes. Add the diced fennel, thyme, garlic and apple. Cover and cook over moderately low heat, stirring occasionally, until softened, about 8 minutes. Add the fennel seeds and cook, stirring, until fragrant, about 1 minute. Stir in the lemon juice, lemon zest, sugar and fennel fronds. Remove the chutney from the heat, season with salt and pepper and let cool to room temperature. Discard the thyme, stir in the bacon and serve the chutney with the toasts.