In 2016, the airline ordered six A320neo models, which was later reduced to three in 2019, and then converted into three orders for the Airbus A321XLR model instead at the beginning of 2020, with plans to launch North American routes. Manufacturer Airbus planned to deliver the planes in 2023 and 2024. However, the airline cancelled the order due to the COVID-19 pandemic.

In October 2017, it was announced that Travel Service planned to transfer its branding from an airline to a holding company, and would move all of its operations under the Smartwings brand. In 2018, it was announced that the Travel Service livery would be replaced by the Smartwings livery. Travel Service was renamed to Smartwings, in December 2018.

From the Autumn of 2018 through the winter of 2019, the Smartwings Group management eliminated many airline routes, including the Prague-Bratislava and Prague-Ostrava routes that the airline has been flying since its inception. Soon after, profitable routes into select Russian cities were eliminated and immediately replaced by new routes operated by Smartwings.

Under the leadership of the Smartwings Group, the Czech Airline's fleet was planned to be transformed into a fully integrated Boeing 737 fleet, the same model that the Smartwings fleet used. However, due to technical and safety issues in the Boeing 737 MAX model found in early 2019, management decided that Czech Airlines would operate the ongoing Airbus fleet while Smartwings would operate a Boeing fleet

In March 2019, Smartwings announced that ČSA would undergo a fleet transition, with the Airbus A319 and ATR 72 to be retired. Then, in the wake of the COVID-19 pandemic, Czech Airlines announced in April 2020 the end of its already suspended sole long-haul route to Seoul. And so, its sole Airbus A330 was to be returned to lessor Korean Air by October 2020.

Towards the end of January 2020, the airline announced a plan to expand and modernize the fleet, with the planned addition of four new Airbus A320s. However, due to the COVID-19 pandemic, these plans were abandoned. In the early stages of the pandemic, the company's workforce declined from 700 to 300 employees, and by the end of the year, the active fleet declined from five planes to two, both of which were under lease, flying to only five European destinations.

During the COVID-19 pandemic, ČSA fell into insolvency, applying for a moratorium in August 2020. In February 2021, a maintenance provider ordered the seizure of two Czech Airlines' ATR 72-500 in Prague over unpaid debts. That same month, the airline notified the Czech Employment Office that it might lay off its entire workforce of some 430 people. In March 2021, it added that it had no means to meet its financial obligations and filed for bankruptcy.

At the end of August 2021, ČSA was operating just one Airbus A320 aircraft; the second was inoperable. As of summer 2022, Czech Airlines had reduced its network to just three scheduled routes. In 2023, the only route operated by Czech Airlines was from Prague-Paris.

In June 2022, ČSA was given a lifeline and exited business restructuring under a new ownership structure. Prague City Air, founded under the aid of Smartwings shareholders, was created to own 70% of ČSA while current majority shareholder Smartwings retained 30%. As of late 2022, the airline also planned to rebuild its fleet and route network using Airbus A320 and newly acquired Airbus A220 aircraft.

On 20 February 2024, Prague City Air s.r.o. purchased 49.92% shares in Smartwings a.s. from Rainbow Wisdom Investment Limited. Smartwings announced that the Czech shareholders now own 100% of the shares in both Smartwings and CSA Czech Airlines.

In October 2024, Czech Airlines was restructured into a holding company, with Smartwings taking over all flight operations under both brand names. The Czech Airlines brand remains active, with two Airbus A320 aircraft in its livery currently in operation. Additionally, four Airbus A220 aircraft in Czech Airlines colours were scheduled for delivery in the upcoming months and maintained the colours of Czech Airlines.

On October 26, the last flight of ČSA (operated as the independent airline) took place, as it took off in the evening from Charles de Gaulle Airport in Paris to Prague Václav Havel Airport. This was the last flight under what has become to be known as its iconic "OK" flight call.

Today, Czech Airlines remains one of the oldest airline brands still flying, despite being owned by a completely different company that once started in 1923. In it's last years, it operated in a markedly reduced and transformed capacity, which was unable to compete effectively with all the Europeans airlines that had already established themselves in the Czech market.

The airline’s historical identity as a full-service Central European network carrier had effectively ended in October 2024.

Today, Czech Airlines lives on not as an independent airline, but as a historic brand after the effective absorption of the airline’s operations into the Smartwings Group. One can only hope that the livery will fly on for many years to come, but with an over increasing changing market and take overs rising over the horizon for the parent company once again, it will be interesting to see the legacy that it will leave behind.