Aircrafts built during the spring were 30 km/h slower than the initial production aircrafts, this partly due to hurry in production leading to rough surfaces, partly to the presence of underwing gun pods, introduced in February.
Many defects were noted during operative use, alongside the already known weak armament, tendency to spin, longitudinal instability and high landing speed:

• sliding canopy difficult to open at speeds over 400 km/h, and this led pilots to usually fly with the canopy open, that reduced the speed by 30 km/h;
• landing gear often failing to extend, and easy to be damaged during landing;
• difficulty to repair damages to the carburettor duct after a belly landing; this could stop to the ground the aircraft for a long time for repair;
• difficulty to repair internal structures of the rear fuselage, because the stabilizator was solidal to them and limited their accessibility;
• unsatisfactory view, particularly during takeoff and landing, due to the long nose and strongly nose-up asset on the ground;
• some splashing of oil on the windscreen reduced the visibility;
• high cockpit temperature, due to the ventral cooler;
• fumes and, eventually fuel vapors in the cockpit;
• lack of a fuel flow indicator;
• low range, particularly with canopy opened, that reduced its utility as a reconaissance plane;
• the unsatisfactory engine acceleration that caused accidents;
• the fall of oil pressure while diving with a negative g load.

The request for a 1000 km range penalized the MiG-3 and LaGG-3, increasing their weight; on the contrary, the Yak-1 never satisfied it, so its flight charachteristics were not impeded by extra weight. In 1941, the only fighter from the Yakovlev OKB that conformed to it was the I-30, that remained as only a prototype.
On May 10, 1941, the ventral tank was reduced from 250 l to 140 l to save weight. Tests on aircraft n. 2859 (with 5 guns) showed that this lightening improved takeoff, landing, turning and horizontal stability; the time of turn was reduced by 2-3 s.
 

On July 10, 1941, automatic slats were introduced, noticeably improving the flight characteristics with regards to spinning.  The introduction of slats led to moving the pitot probe from the right wing edge to the lower right wing surface.

In the seconf half of 1941 the engine gear reduction ratio changed from 0.902 to 0.732, and this was associated with a new AV-5L-123 propeller instead of VISh-22E; the new propeller blades had a pitch angle range of  30° instead of  20°. They are not distinguishable in photos. Late MiG-3s could have both gear ratios; the installed one was painted on the cowling side to avoid mistakes while mounting the propeller.  (left) An armoured glass was installed internally to the windshield.  It is difficult to recognize on photos, so it is difficult to determine this was common.  (right)

On some examples, a system to fill tanks with inert gas was installed; this is recognizable from a small pipe taking exhaust gases from the 2nd and 3rd left exhaust stacks. The purpose of this system was to exclude air in the tanks, reducing oxigen on them with obvious safety benefits. This system, although required by early test pilots since 1940, was frequently installed on examples built in summer 1941 and later.

On April 12, 1941, the order NKAP n.322 ordered to increase the daily production of MiG-3 to 20 examples, starting from August; this increased the projected output of MiG-3s during 1941 to 4295 aircrafts.
 

In May 1941, the control surfaces were modified by increasing to 26% of the aileron compensation, and modifying horizontal tail assembly with a smaller stabilizer (63% of total area) and enlarged elevator (37% of total area). These modifies were tested on 5 examples (nr.3205, 3211, 3214, 3120 and 3169) and approved, but the war prevented their implementation on series aircrafts.

The engine cowling with dzus locks was considered unsatisfactory and too complex by first line units; according to this, a new cowling inspired to that of Bf-109 was tested at first on the aircraft n.2554, and then introduced into series production from the 16th series (each series was usually composed of 100 aircrafts, so the new cowling should be installed from the aircraft n.3600).

Visible modifications between typical early MiG-3 and typical late MiG-3 were:

the different scomposition of the engine cowling, particularly the upper part that became in one piece and locked with lever locks instead of Dzud locks; the new cowling had two longitudinal fairings for lateral gun barrels; this allowed to replace the side ShKAS with larger guns as UBS or ShVAK without alteration of the external paneling (this modify of armament was made on few late examples only);

Left: early type (early characteristics marked with light blue).

Right, late type (late characteristics marked with pink).

the addition of small horizontal triangular plates on the oil coolers outlet to improve aereodynamicity when shutter is in open position; the modify of exhaust stacks, that received a typical fairing covering almost completely the first stack, and upper and lower plate lips; the introduction of a gap behind the stacks; this was due to the moving back of the cowling border to improve the access to the engine, but can give the impression that the aircraft was lenghtened, so the late MiG-3 is sometimes erroneously called "long-nosed", "leghtened" or "MiG-3 UD"; in reality, the total lenght remained 8250 mm; the side plates behind the engine were shortened, and the grilles on them were suppressed; the introduction of fully closed and bulged doors for tail wheel.

Automatic shutters were introduced in the supercharger intakes on the wing roots to avoid dust ingestion; they were actioned by the undercarriage retraction and extraction.  (left) On the earlier aircrafts, only a grille prevents foreign matter ingestion. (right)

On many later examples, forthemost observed during winter 1941/42, the tail wheel was fixed in lower position, while the doors were removed and replaced by a canvas cover; it is not clear if this was made in the factory or on the field.

The horizontal stabilizators were modified, apparently enlarging their chord at the tip.

 

On some late examples, a starter tooth was introduced, protruding from the spinner point; differently than on other aircrafts, no any macroscopic step or slot is visible between spinner and tooth.

During the summer 1941, tests were made on many armament combinations:

• 2 UBS and 2 ShKAS;
• 2 UBS and 1 ShKAS;
• 2 UBS.

This interesting perspective shows the example n. 5015 produced on late 1941, armed by two machine guns UBS and two built-in batteries of ZROB-82 for the shooting rocket projectiles ROS -82.