Bowler said he was sad to be leaving but said he felt the time was right.
"When I look back at my time with the business, I'm most proud of the way our team has worked together tirelessly through the uncertainties of the pandemic and still achieved all of its pre-listing forecasts in the 2021 and 2022 years," he said.
Bowler's final day is October 14.
The board is commencing a search for Bowler's replacement.
Chief financial officer Mark Winter will act as the interim CEO following Bowler's departure.
My Food Bag shares have been a major disappointment since investors bought into the IPO in March 2021 at $1.85, allowing existing shareholders to sell down their holdings.
The stock last traded at 63c, down one cent.
In a trading update issued in August, the company said it had seen a slower start to trading in 2023 than expected.
As of the end of July, deliveries were down 3.8 per cent compared to the same time last year.
At the same point, active customer numbers had recovered from the beginning of the year to be 73,145 - in line with the end of July 2021 figure 72,105.
"Omicron had a marked effect on My Food Bag's supply-side confidence in Q4 2022 as the company and its suppliers encountered difficulties accessing staff and dealing with the flow-on problems of incomplete and late deliveries," the company said then.
"My Food Bag responded to these challenges at the time by further simplifying its product offering and reducing marketing activity, which had the effect of a slower start to 2023," it said.
"As a consequence of the lower earnings performance to date and anticipated impact from ongoing economic headwinds, full-year earnings for the current year are expected to be below 2022," the company said.
