During the mid-1980s Embraer was working on the Short Tucano alongside a new version designed EMB-312G1, carrying the same Garrett engine. The EMB-312G1 prototype flew for the first time in July 1986. However, the project was dropped because the Brazilian Air Force was not interested in it. Nonetheless, the lessons from recent combat use of the aircraft in Peru and Venezuela led Embraer to keep up the studies. Besides a trainer, it researched a helicopter attack version designed "Helicopter killer" or EMB-312H. The study was stimulated by the unsuccessful bid for the US military Joint Primary Aircraft Training System (JPATS) program. A proof-of-concept prototype, the PT-ZTW flew for the first time in September 1991, the aircraft features a 1.37-meter (4.49-ft) fuselage extension with the addition of sections before and after of the cockpit to restore its center of gravity and stability, a strengthened airframe, cockpit pressurization and stretched nose to house the more powerful PT6A-67R (1,424 Shp) engine. Two new prototypes with the PT6A-68A (1,250 Shp) engine were built in 1993. The second prototype flew for the first time in May 1993 and the third prototype flew in October 1993.
The request for a light attack aircraft was part of the Brazilian government's SIVAM (Amazon Surveillance System) Project. This aircraft would fly with the R-99A and R-99B aircraft then in service and be used to intercept illegal aircraft flights and patrol Brazil's borders. The ALX Project was then created by the Brazilian Air Force, which was also in need of a military trainer to replace the Embraer EMB 326GB Xavante. The new aircraft was to be suited to the Amazon region (high temperature, moisture, and precipitation; low threat). The ALX was then specified as a turboprop engine aircraft with a long range and autonomy, able to operate in night and day, in any meteorological conditions, and able to land on short airfields lacking infrastructure.
In August 1995, the Brazilian Ministry of Aeronautics awarded Embraer a $50 million contract for ALX development. Two EMB-312H were updated to serve as ALX prototypes. These made their initial flights in their new configuration in 1996 and 1997, respectively. The initial flight of a production-configured ALX, further modified from one of the prototypes, occurred in 2 June 1999. The second prototype brought up to two-seater configuration and performing its first flight on 22 October 1999. The changes had been so considerable that the type was given a new designation, the "EMB-314 Super Tucano". The total cost of the aircraft development was quoted to be between US$200 million and US$300 million.
The aircraft differs from the baseline EMB-312 Tucano trainer aircraft in several respects. It is powered by a more powerful 1,200 kW (1,600 shp) Pratt & Whitney Canada PT6A-68C engine (compared to the EMB-312's 560 kW (750 shp) powerplant); has a strengthened airframe to sustain higher g loads and increase fatigue life to 18,000–12,000 hours in operational environments; a reinforced landing gear to handle greater takeoff weights and heavier stores load, up to 1,550 kilograms (3,300 pounds); Kevlar armour protection; two internal wing-mounted .50 calibre machine guns (with 200 rounds of ammunition each); capacity to carry various ordnance on five weapon hardpoints including Giat NC621 20 mm cannon pods, Mk 81/82 bombs, MAA-1 Piranha air-to-air missiles (AAMs), BLG-252 cluster bombs and SBAT-70/19 or LAU-68A/G rocket pods on its underwing stations; and has a night-vision goggle (NVG)-compatible "glass cockpit" with hands-on-throttle-and-stick (HOTAS) controls; provision for a datalink; a video camera and recorder; an embedded mission-planning capability; forward-looking infrared (FLIR); chaff/flare dispensers; missile approach warning receiver systems (MAWS) and radar warning receivers (RWRs); zero-zero ejection seats. The structure is corrosion-protected and the side-hinged canopy has a windshield able to withstand bird strike impacts up to 500 km/h (270 kn).
In 1996, Embraer selected the Israeli firm Elbit Systems to supply the mission avionics for the ALX. For this contract, Elbit was chosen over GEC-Marconi and Sextant Avionique. The Israeli company supplies such equipment as the mission computer, head-up displays, and navigation and stores management systems.
On 13 October 2010, the Super Tucano A-29B had passed the mark of 48,000 hours since 21 July 2005 on full scale wing-fuselage structural fatigue test, conducted by the Aeronautical Systems Division (ASA), part of the Aeronautics and Space Institute (IAE) at the Structural Testing Laboratory. The test involves a complex system of hydraulics and tabs that apply pressure to aircraft structure, simulating air pressure from flying at varying altitudes. The simulation continued for another year to complete the engine fatigue life test and crack propagation studies for a damage tolerance analysis program of conducted by Embraer and IAE/ASA.
Embraer developed an advanced training and support system suite called Training Operational Support System (TOSS) an integrated computational tool composed of four systems: Computer Based Training (CBT) enabling the student to rehearse the next sortie on a computer simulation; Aviation Mission Planning Station (AMPS) which uses the 3D visuals to practice planned missions and to check inter-visibility between aircraft and from aircraft and other entities; Mission Debriefing Station (MDS) employs real aircraft data to playback missions for review and analysis; Flight Simulator (FS). MPS and MDS was enhanced with MAK’s 3D visualization solution to support airforces pre-existing data, including GIS, Web-based servers and a plug-in for custom terrain formats.
In 2012, Boeing Defense, Space & Security was selected to integrate Joint Direct Attack Munition (JDAM) and Small Diameter Bombs (SDB) for the Super Tucano. In 2013, Embraer Defense and Security CEO disclosed that its subsidiary, OrbiSat, was developing a new radar for the Super Tucano. A Colombian General disclosed that the future Side looking airborne radar (SLAR) will be able to locate ground targets smaller than a car with digital precision.