By summer 1941, most of the units equipped with the Dornier Do 17 were upgrading to the Ju 88. With a few exceptions, most of the German bomber units were now flying the He 111 and Ju 88. The Ju 88 was to prove a very capable and valuable asset to the Luftwaffe in the east. The Ju 88 units met with instant success, attacking enemy airfields and positions at low level and causing enormous losses for little damage in return. 3./Kampfgeschwader 3 attacked Pinsk airfield in the morning of the 22 June 1941. It caught, and claimed destroyed, 60 Soviet bombers on the ground. The 39 SBAP Regiment of the 10 Division SAD actually lost 43 Tupolev SBa and five Petlyakov Pe-2s. Ju 88s from Kampfgeschwader 51 destroyed over 100 aircraft after dispatching 80 Ju 88s to hit airfields. In general the Soviet aircraft were not dispersed and the Luftwaffe found them easy targets. A report from the Soviet 23rd Tank Division of the 12th Armoured Corps reported a low-level attack by Ju 88s on 22 June, resulting in the loss of 40 tanks. However, the Ju 88s were to suffer steady attritional losses. At 0415 on 22 June 1941, III./KG 51 attacked the airfield at Kurovitsa. Despite destroying 34 Polikarpov I-153s, the Ju 88s were intercepted by 66 ShAP I-153s. Six Ju 88s were shot down before the German fighter escort dealt with the threat. By the end of the first day of the campaign, Ju 88 losses amounted to 23 destroyed.
Due to the lack of sufficient numbers of Ju 87 Stukas, the Ju 88 was employed in the direct ground support role. This resulted in severe losses from ground fire. Kampfgeschwader 1, Kampfgeschwader 76 and Kampfgeschwader 77 reported the loss of 18 Ju 88s over enemy territory on 23 June. KG 76 and KG 77 reported the loss of a further four Ju 88s, of which 12 were 100% destroyed. In the north, the VVS North-Western Front lost 465 aircraft on the ground, 148 of them bombers, to the Ju 88s of KG 1. A further 33 were damaged. Out of a total of 1,720 aircraft deployed by the VVS Northern Front on 22 June, it lost 890 and a further 187 suffered battle damage in eight days.[28] The Ju 88s units helped virtually destroy Soviet airpower in the northern sector. Again, the Ju 88 demonstrated its dive-bombing capability. Along with He 111s from KG 55, Ju 88s from KG 51 and 54 destroyed some 220 trucks and 40 tanks on 1 July, which helped repulse the Soviet South Western Front's offensive. The Ju 88s destroyed most rail links during interdiction missions in the area, allowing Panzergruppe 1 to maintain the pace of its advance.
Ju 88 units operating over the Baltic states during the battle for Estonia inflicted severe losses on Soviet shipping, with the same dive-bombing tactics used over Norway, France and Britain. KGr 806 sank the Soviet destroyer Karl Marx on 8 August 1941 in Loksa Bay Tallinn. On 28 August the Ju 88s had more success when KG 77 and KGr 806 sank the 2,026 grt steamer Vironia, the 2,317 grt Lucerne, the 1,423 grt Artis Kronvalds and the ice breaker Krisjanis Valdemars (2,250 grt). The rest of the Soviet "fleet", were forced to change course. This took them through a heavily mined area. As a result, 21 Soviet warships, including five destroyers, struck mines and sank. On 29 August, the Ju 88s accounted for the transport ships Vtoraya Pyatiletka (3,974 grt), Kalpaks (2,190 grt) and Leningradsovet (1,270 grt) sunk. Furthermore, the ships Ivan Papanin, Saule, Kazakhstan and the Serp i Molot were damaged. Some 5,000 Soviet soldiers were lost.