For two years now, I've been playing around to see how little I could get away with on over-wintering pepper plants.
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I've come to at least two conclusions.
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First, yeah, it's best to uproot them and put them in fresh soil. I'm sure a master gardener can work around this, but the easiest way is to pluck them out, and put in fresh soil.
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Second, there's pro's and con's to over-wintering. If you do it right, you'll get a good crop the next year (especially if you started too late to get any reasonable crop out of the year before). But, you're highly likely to be over-wintering the pests as well as the peppers. Speaking personally, the aphids seemed to greatly appreciate the warmth and care I bestowed on my over-wintered peppers. I suspect I'm lucky that, so far, it's only been aphids.
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And, at the end of the year, the crop you get out of starting from seed (if done correctly) will have you wondering if over-wintering gets you more peppers. You'll get more peppers early from the over-winter, but the final tally is often a toss-up.