Shakespeare, 44, joined Albion nine years ago as a recruitment officer before becoming youth-team coach under then-manager Gary Megson and subsequently reserve-team boss.
Baggies boss Tony Mowbray said: "We are sorry to see Craig leave. He contributed greatly to our success last season but we didn´t want to stand in his way. He feels it is an opportunity to progress his career from being a coach to an assistant manager, and it is a good opportunity for him."
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