Prepare a boiling water bath canner and and enough jars to hold 4 pints worth of product.
Fit a food processor with a grating blade and use it to break down the fennel, zucchini, green peppers, and onion. If you don't have a food processor, pull out your trusty box grater and get to work.
Combine fennel, zucchini, pepper, and onion shred with the vinegar, brown sugar, mustard seeds, salt, fennel seeds, and red chili flakes in a large pot and bring to a boil.
Cook the relish at a boil for 2 to 3 minutes, until the liquid has reduced some.
Add lemon zest and juice and stir to combine.
Remove relish from the heat and funnel it into prepared jars, leaving approximately 1/2 inch headspace.
Bubble jars well. Wipe rims, apply lids and rings, and process jars in a boiling water bath canner for 10 minutes.
When time is up, remove jars from canner and place them on a folded kitchen towel to cool.