By the summer of 1943, due to growing production volume and a general decrease in quality, the basic performance characteristics of production bombers had degraded to an intolerable level. The Factory No. 22 designers were tasked with drastically improving the quality of the bombers produced. The new chief designer, V. M. Myasishchev, was in charge of this work.
The Factory No. 22 designers, together with the researchers of the Central Aerohydrodynamic Institute (TsAGI), proposed a number of improvements for the Pe-2 design that were implemented in production in August 1943, beginning with series 205. Improvements were made to the flaps, cowls, and access doors, pressurization of the whole aircraft was ensured, the shape of the cooler ducts was altered, and carburettor inlet ducts with improved aerodynamics were installed. Brake cover fairings and a new single-blade compensator (with an increased area) for the VUB-1 turret were also installed. The radio antenna mast, together with the airspeed tube, was removed to the front arch of the cockpit canopy, and the junction of the canopy and the VUB-1 turret was improved. Some planes had individual exhaust pipes installed instead of the previous general exhaust manifolds.
Beginning with series 211, the beams of external bomb racks were moved into the wings, and beginning with series 249, it was decided that the oil should be diluted with gasoline in the winter. From series 265 on, the RSB-bis radio set was replaced with an RSB-3bis, and the general antenna-feeder system was improved, drastically increasing radio coverage. Series 275 saw yet another reinforcement of the Pe-2's rear defense: a DAG-10 grenade launcher was installed, with 10 AG-2 aerial grenades. The grenades were housed in the radio operator/gunner's cockpit in two clusters (five in each). A grenade launched from the aircraft would initially reduce speed (with a small parachute) and then, after a delay of 3 to 5 seconds, explode in the path of a pursuing fighter. The grenade launcher gave the gunner a chance to stop German fighters from comfortably attacking the Pe-2 from their favorite position, the rear.
Crews noted the bomber's high maneuverability and survivability, the good field of view from the cockpit, and good stability during dives. At the same time, though, it was noted that the aircraft was rather difficult to pilot, especially when taking off and landing.