English League One club Fleetwood and the League of Ireland First Division side Waterford, both owned by Andy Pilley, hired Walters in a combined Technical Director position in December 2022.
Walters, who made 233 Premier League appearances as a player, had previously served as the Senior Men's Scout and Under-19s Assistant for the Football Association of Ireland.
After seeing Fleetwood draw 2-2 with Ipswich Town to finish 13th in League One at the weekend, Walters announced his departure on Instagram, saying: "As we come to the end of the EFL season, I feel the time is right to step down from my role as Technical Director of Fleetwood Town and Waterford FC.
"Together, with the support of many great people, we have strengthened the Fleetwood squad, comfortably secured League One status and made history by taking the club to the 5th Round of the FA Cup.
"With Waterford, I was delighted to help implement some new structures and bring in two fantastic people in [Manager] Keith Long and [Assistant Manager] Alan Reynolds, whom I have no doubt will bring success back to the club."
At the time of Walters' appointment in December, Pilley said: "Jonathan is an experienced and knowledgeable character who can help the club move to the next level in structure, recruitment, and sporting success on the pitch."
Photo courtesy of Fleetwood Town FC
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