1. Trills. In most of Bach‘s pieces, all trills must start on the upper note on the beat. However, I see some people playing from the main note and even starting before the beat. In other words, they start the trills too early. One thing that helps me to play these trills correctly is constantly keeping your attention on the pulse and then it's easier not to start the trill too early.
2. Articulation. The touch which many people transfer from piano to the organ is legato and in such music is not the ideal one. The manner of playing should be smooth and singable (cantabile) but there should be definitely small spaces between each note (unless indicated otherwise by the composer). We call it articulate legato.
3. Pedaling. Another important mistake is using the heels when playing the pedal part in Bach‘s organ pieces. It seems easier for a lot of people but in reality, this manner of playing produces legato touch which is not used for this type of music.
4. Practicing. If you are used to play Bach‘s pieces from the beginning until the end without stopping, I recommend you reconsider this method. The best option would be to stop whenever you make mistake, go back a few measures and correct it several times. Playing in shorter fragments often is more beneficial than playing without stopping.
5. Fingering. Many people still use finger substitution in Bach‘s organ works which I don't recommend. You see, finger substitution technique was developed to create the legato touch which is not stylistically correct manner of playing.
6. Feeling of the pulse. This is a critical mistake, without feeling the pulse and alternation of strong and weak beats, your performance will be dragging and lacking the natural flow. I recommend to shorten the weak beats and play the strong beats longer.
7. Suspensions. A lot of times people make this mistake. Even when they articulate the piece correctly, they might make rests after suspensions. In other words, they might make an eighth note rest after a tied-over note. The correct way to play it is to hold this note longer and play the next note almost legato.
8. Registration. Way too many people play Bach‘s free works (preludes, fugues, fantasias, toccatas etc.) changing registration too often. In free works (not chorale based pieces) you should use Organo Pleno registration on one or more manuals (full principal chorus).
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