The world's oldest travel firm secured a rescue package from its lenders late on Friday following days of frantic talks, but analysts say the damage is already severe.
Trading was challenging enough, but this could have been further exacerbated by the events of the past week, said analyst Nick Batram at brokerage Peel Hunt.
Shares in Europe's second-biggest travel firm by sales rose by as much as two-thirds in early trade on Monday, although the gains were partially pegged back as investors digested details of the travel firm's emergency loan.
The stock, which has lost nearly 90 percent of its value over the past year, was up 19 percent at 21.3 pence as London's stock market closed on Monday.
The company's battered bonds -- a 7.75 percent 300 million pound 2017 issue and a 6.75 percent 400 million euro (343.4 million pound) bond maturing in 2015 -- recovered to around 48 pence in the pound, according to Tradeweb, having sunk to 30 last week.
Its traded loans, a 1 billion pound facility made up of 850 million in revolving credit and a 150 million pound term loan, were bid at 80 pence in the pound.
These debts and bonds, plus a 200 million pound bonding facility for guaranteeing flight bookings, along with the new 200 million pound emergency facility, bring Thomas Cook's total outstanding debt to as much as 2.1 billion pounds.
Thomas Cook, which had issued a string of profit warnings over the past year, blamed the slump in bookings by British customers on uncertainty over the company's future.
We were down 30 percent on bookings which is of course substantial but ... it could have been much more had our customers not shown loyalty to us, Acting Chief Executive Sam Weihagen told the BBC in an interview on Saturday.
Thomas Cook said on Friday its banks, led by Barclays
Thomas Cook will pay about 6 percent interest on the loan, rising 0.5 percent every quarter -- which analyst James Hollins at brokerage Evolution said was a high price but not extortionate.
Hollins estimates the new facility pushes Thomas Cook's gross debt up to around 1.5 billion pounds, but said the timing of the company's latest difficulties gives it time to restore confidence ahead of the post-Christmas booking period.
Fortunately, all the bad press has come at a relative low point in the booking cycle and the group has the funds and time to restore partner and consumer confidence in its brand and survival, Hollins said.
The company, which takes over 22 million people on holiday each year, had asked its lenders to come to its rescue for the second time in five weeks last Tuesday.
It has now embarked on a strategic review as it looks to bring down its debt. It has already announced plans to raise 200 million pounds through disposals and analysts expect it to close hundreds of shops.
Tour operators have struggled as the emergence of low-cost airlines and the Internet led to more holidaymakers booking online. Thomas Cook's core customer base of families with young children has also been hard hit by tough economic conditions, while bookings were impacted by unrest in popular destinations such as Egypt, Tunisia and Morocco.
Peel Hunt's Batram said the recapitalisation of the business is likely to be painful and it will need an equity fundraising.
Institutions are likely to be asked to contribute to an equity refinancing and back a management team where credibility has been damaged, he said, adding the company may need to raise another 600 million pounds.
The company is searching for a new chief executive after industry veteran Manny Fontenla-Novoa quit in August. Thomas Cook had issued a string of profit warnings and last week delayed publication of its full-year results.
(Additional reporting by Natalie Harrison and Tessa Walsh; Editing by David Holmes and Andrew Callus)