Releasing its 2018/19 H1 trading statement, the airline said it had weathered year-on-year cost increases of about £17 million due to the combined effect of the falling pound and rising fuel prices.
However, the airline added that the two issues combined with weakening demand would cost the airline a total of £29 million.
This would lead it to record a full year adjusted loss before tax of £12 million and comes despite the airline receiving about £10 million for the return of leased aircraft.
Flybe chief executive Christine Ourmieres-Widener said: "We have made progress in driving our unit revenues across the summer season, but we are now seeing a softening in the market.
"We are reviewing further capacity and cost saving measures while continuing to focus on delivering our sustainable business improvement plan.
"Stronger cost discipline is starting to have a positive impact across the business, but we aim to do more in the coming months, particularly against the headwinds of currency and fuel costs.
"We continue to strengthen the underlying business and remain confident that our strategy will improve performance."
The news comes after the airline reported an eight percentage point increase in load factor to 84% for the first half of the year while passenger revenue per seat grew by 8% in the same period.
This led it to predict its adjusted profit before tax for HA would be similar to the previous year when it recorded £9.4 million.
The airline had a total fleet size of 78 aircraft as of September 30.