On 20 April 2012, the Boeing 737-236A aircraft serving the route crashed in bad weather during the final approach killing all 121 passengers and 6 crew on board, it remains as the second deadliest air disaster in Pakistan.

Additionally, Bhoja Air's lack of oversight and multiple errors within Pakistan CAA's monitoring system of Pakistani airliners further contributed to the accident.

First Officer Malik later suggested that they should go towards the right (east) to avoid the storm system, but Captain Afridi refused, insisting that they should land at Islamabad.

[7][4]: 8–22 Controller in Islamabad later cleared Flight 213 to land, however due to the chaotic situation inside the cockpit the crew never acknowledged the call.

It crashed at a distance of 4.24 nautical miles (4.88 mi; 7.85 km) from the runway, in the small village of Hussainabad in Rawalpindi, in heavy rain condition.

[21][4] A statement on Bhoja Air's website offered condolences to the affected families and said that it would fulfil its legal obligations under the Pakistani law applicable at the time of the accident.

[16][24] President Asif Ali Zardari cut short his trip to cities in Punjab and returned to the capital, and he and Prime Minister Yousuf Raza Gillani sent condolences to the families of those who died in the accident.

The Civil Aviation Authority issued an office order at 9 a.m. the next day, requiring all airlines to transport the bodies of the victims free of cost.

[29] On 28 May 2012, Bhoja Air's license was revoked by the CAA, due to failing a requirement under the Pakistani Civil Aviation laws that a carrier must maintain a minimum fleet of three aircraft.

[35] The corruption within CAA, due to politically motivated appointments, was alleged to be the prime reason for the increase in frequency of technical faults, crash landings and catastrophic air accidents.

[4]: 36–41, 49–55 Data from numerical weather prediction products on the day of the accident showed that a westerly wave was injecting cool air from the northwest, while winds from the Arabian Sea in the south of the country fed warm moisture into the upper part of Pakistan.

Interaction between both air masses eventually produced severe thunderstorms in the area, which resulted in the creation of strong updrafts and downdrafts.

Images taken at 14:00 local time depicted a development of a severe weather system over the central part of Khyber Pakhtunkhwa, which slowly migrated towards the east and then northeast.

Radar echoes revealed a frontal weather activity which generated severe turbulence and wind shear, which were attributed to the development of microbursts.

[4]: 36–41, 49–55 Analysis of the obtained data concluded that a strong wind shear and a converging system approached Islamabad's Benazir Bhutto International Airport from the southwest, which intensified at around 18:00 to 19:00 local time.

[4]: 36–41, 49–55 Information regarding the weather condition in Islamabad was continuously updated by authorities from the airport's meteorological department, and was relayed to the controller so that it could be communicated to the crew of Flight 213.

[4]: 36–41, 49–55 In accordance with Bhoja Air's written manual, the crew should have abandoned the approach to Islamabad due to the deteriorating weather conditions.

During the approach phase, the crew requested clearance to deviate from their track in order to penetrate a group of cumulonimbus clouds through a small gap.

Bhoja Air had previously been suspended due to financial difficulties in the early 2000s and had been recently relaunched in March 2012, just a month earlier.

First Officer Malik was noted as being "ignorant" of the alarms as he was busy with the communication between Flight 213 and the controller, instead of assisting the captain, who had been severely pre-occupied with the dangerous weather condition for quite some time.

The limited thrust setting, landing configuration of the aircraft, and the rapid pitch up, subsequently caused the stall warning to activate.

The aircraft was already at an unusually low altitude and the captain's decision to put the nose in a steep position caused the GPWS to sound.

Both pilots met for the first time in Pakistan Air Force Academy, with Captain Afridi as the flight instructor and First Officer Malik as a cadet.

Civil Aviation Authority requested Bhoja Air to submit the ground schooling curriculum for cockpit crew of the Boeing 737-200 series.

[4]: 27–29 Captain Afridi had undergone his recurrent simulator training in a British Airways Comair facility in South Africa in January 2012.

Due to the absence of such training, the captain sought refuge from the aircraft's automation to provide him a solution when he should have followed the recommended procedures from Boeing.

Bhoja Air had not provided the manual for the Boeing 737-200A, had not implemented any recommendations that had been given by the South African flight instructor, and had not established a monitoring system to track the cockpit crew's performance at organizational level.

[4]: 27–28 The CAA inspector, who was responsible for Bhoja Air, was qualified but did not have any experience on the Boeing 737-200 and therefore they could not conduct an observation on the automated flight deck training.

The report also found that the ineffective automated flight deck management in extreme adverse weather conditions by the cockpit crew caused the accident.

The inability of the CAA to ensure automated flight deck variance type training and monitoring requirements primarily due to incorrect information that had been provided by Bhoja Air was listed as one of the contributing factors to the crash.