The answer is simple: make use of pedal preparation technique. Here is how it works.
As soon as you release the note with one foot, slide it in place for the next note of the same foot with one swift motion. Don't depress the new note yet but let it wait for it's turn. Do the same with another foot for the entire pedal line of your organ piece.
If you tried it on your organ, you would soon discover that at first you really have to think about the next note and its preparation. So now you might have an obvious question - how many times should you repeat the pedal passage to make it fully automatic?
What I have found from my personal practice is that I need to repeat a small pedal fragment (about 4 measures) in a slow fully controlled tempo 10 times for 10 days in a row. That makes a total number of 100 repetitions (more in cases for extremely difficult music).
This make sense when you think that it takes about 80-100 times of repetitions of the word in a foreign language to fully sink in in our long-term memory.
If you haven't ever used this organ technique in your pedal playing, I encourage you to try it out. Make a little experiment. During the period of the next 10 days, learn one passage of pedal part with pedal preparation and another passage of similar length and difficulty without it. You will be amazed when you compare your fluency of both passages.
By the way, do you want to learn my special powerful techniques which help me to master any piece of organ music up to 10 times faster? If so, download my video Organ Practice Guide.