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What's the proper way to fit a hybrid/commuter bike?

Most detailed bike fit articles seem to apply to road bikes but not so much for hybrid/commuter bikes which cycle commuters, recreational cyclists, and weekend warriors often use. A good bike fit can encourage cycling for transportation, improve fitness and health, and shorten trip times because it increases comfort, reduces injuries, improves power output, and reduces the risk of neglected muscle groups while exercising.

From what I learned, posture actually affects which muscle groups are emphasized. It's about as important as learning how to pedal properly. Using more of our muscle groups can increase endurance and power. It may even improve blood pressure responses during exercise which is especially important for those with a heart condition. A study showed that exercising with our arms led to higher BP than exercising our legs. Arms have smaller muscle groups than legs. They should have fewer capillaries too so the heart has to work harder at the same blood flow. Rolling our hips forward increases glute utilization. With a good bike fit, it's easier to pedal smoothly.

For hybrid bike fitting, can we determine the saddle height by the 30 degree knee angle, heel on pedal with the knee straight, or 109% method?

Would the knee over pedal spindle method be reasonable?

How do you know that the stem length and angle is correct? Road bike fitting often have the back angle at 45 degrees, and the shoulder angle at 90 degree but what should they be for a hybrid bike fit?

Since hybrid/commuter bikes don't have drop bars, should a mountain bike fit be used instead?

Hybrids are very similar to hardtail mountain bikes in their geometry, but a significant difference is the width of the bars: the hands can be much further apart on a mountain bike (as sold, my MTB was 100mm wider between the grips than my hybrid, now it's more like 150). Even allowing for a change in elbow angle, this will have knock-on effects on reach.

Another difference is that MTBs tend to be set up with a low saddle despite the high bottom bracket, as the rider needs to often stand with bent knees. This isn't suitable for hybrids in general, and one of the first things to do when converting a mountain bike from trail use to commuting is to raise the saddle. This will then affect the desired stack (and reach). A high saddle over a high BB will make the ground a long way down when the saddle height is "correct" (for efficiency and knee health). If this makes stop-start riding tricky, it will have the opposite effect to that desired. Luckily hybrids tend to have a slightly lower BB than mountain bikes, and thinner tyres, so this isn't necessarily an issue. (This one is a bit personal as having a child seat on the back makes holding and starting the bike harder with a significant lean, and also means that getting going from standing over the toptube is harder)

As a fit for comfort (rather than performance) is desired, it's possible that an MTB fit would be too aggressive anyway, and although efficiency is desirable, the difference between an OK fit and a perfect fit won't be noticeable on most hybrid journeys.

Comfort fits are rather subjective anyway(so measurements will only get you part of the way), but it takes a fairly long ride to get a feel for the last little bit.

As an example, I bought a hybrid and used it for occasional day rides before starting a 15km each way commute. It was the right nominal size and all I did was adjust the saddle height and fore-aft position (the latter because I slid forwards). Only when I started doing rides of 3-4 hours (up to 70 km) did I do anything to the reach/stack, and also made the bars narrower.

Setting the seat height and setback relative to the bottom bracket using the same ballpark methods for road bikes is probably a good start. Road bike seat height will give a good, comfortable range of motion for the legs and prevent the knees coming up too high at the top of the pedal stroke.

I suspect that with more upright torso positions, the seat should move back a little, to rotate the whole body around the pedals, rather than just rotate the torso at the hips. (This would be the opposite of what is done for time trial, horizontal back positions where the seat is moved forward.)

There is no correct back angle for hybrid bikes (there isn't for road bikes either). The back angle is determined by the 'aggressiveness' or 'comfortableness' of the frame and handlebars stack and reach geometry. Really there is a continuum of bike cockpit geometries from time trial machines through road bikes, flat bar commuters and hybrids to dutch bikes and beach cruisers.