Faceliften kom i 2001..
For the 2001 model year, BMW updated the E39 with newer, clear-lens tail, side marker, and headlights which first displayed the now-popular "angel eyes." Rear tail lights were changed to LEDs (Hella, the OEM, refers to these lights as "CELIS"), while the side and rear turn signals were changed from amber lenses to clear. The black trim was now painted to match the body color, and the front bumper now featured rounded fog lights. Internally many changes were made to electronics; items such as window regulators and the air conditioning were updated. The 528i was replaced by the 530i which had a new 168 kW (225 hp) M54B30 3.0 L inline-6. A new entry-level 525i was introduced featuring a 137 kW (184 hp) M54B25 2.5 L I6 and a slightly lower price. The available navigation system was changed to a wide screen version.
2002
In 2002, BMW Steptronic-equipped E39s had their manual shift direction switched to match BMW's SMG. Also, in 2002 the 540i V8 32V engine power was increased from 210 kW (282 hp) to 216 kW (290 hp) while torque remained the same. All models got a standard in-dash CD player, 6-cylinder models added a standard power passenger seat, and the 525i received automatic climate control standard. Consumer Reports declared the 2002 BMW E39 the best car they had ever reviewed.
2003
2003 marked the last year for the E39 platform; they were differentiated by the addition of extra chrome trim on the trunk (boot) and on the sides of the body. In all 6-cylinder model 5-Series add a standard sunroof. The optional navigation systems upgraded from CD-ROM format (8 CDs to cover the entire USA and Canada) to single DVD-ROM. The optional sport package on the 540i carried parts from M-technic. This included a full M-tech ground effects, M-tech II suspension, 18 inch wheels, and a variety of M badging. The E39 wagon (touring / estate) was continued into the 2004 model year until the touring version of the new E60 5 Series was released.