Sky News has seen some of the emails, which mainly come from longer-term workers, who say they have been hit hard by the changes.
In one, a worker at a fulfilment centre in Dunfermline warns Mr Bezos that the move "may receive major backlash and some disappointed workers".
The email continues: "We take great pleasure in receiving our shares as that is what makes amazon unique and for people that have children it is a delight to have that extra bonus."
In another, a worker who says they have worked for seven years in Amazon's fulfilment centre at Doncaster, tells Mr Bezos: "It's great looking forward to receiving our shares/share on a yearly basis... It pays for a well-earned holiday which I wouldn't be able to pay for without."
Another worker, who says they have worked for Amazon for nine years, voices anger, writing to Bezos: "You say you listened to us! But when did we get to vote on the change of pay."
However, the dominant note among the 41 emails is disappointment.
As one worker puts it in their email: "I would hope you have the time to recognise that people are upset… We respect the values of the company. And do our best every day in hope of recognition."
Sky News has not revealed the names of the workers, some of whom say their public statements could create difficulties
Amazon, which has faced heavy criticism over its treatment of its lowest-paid workers, announced on 2 October that it was increasing its minimum hourly pay in the US and UK.
Minimum pay for permanent and temporary staff in the UK outside London was raised by £1.50 an hour to £9.50. In the capital it was raised by £2.20 to £10.50.
However, the GMB union accused the firm of subsidising the pay rise by cutting a share scheme for warehouse workers, which entitles them to one share - currently worth ($1,885) £1,435 - for every year they work at Amazon, with an additional share once every five years.
After two years, according to the GMB, workers can cash in the shares - known as restricted stock units, or RSUs - for free.
In a blogpost announcing the change, Amazon said that it was phasing out RSUs because "we've heard from our hourly fulfillment and customer service employees that they prefer the predictability and immediacy of cash".
The firm told Sky News: "The significant increase in hourly cash wages more than compensates for the phase out of RSUs.
"We can confirm that all hourly Operations and Customer Service employees will see an increase in their total compensation as a result of this announcement. In addition, the compensation will be more immediate and predictable."
The email campaign has been conducted through Organise, a website for workplace campaigns set up in 2017.
A petition launched on the site immediately after Amazon's announcement gathered around 1200 signatures, according to Organise.
The signatories then voted to send emails to Bezos, rather than taking the more confrontational step of delivering their petition to Amazon headquarters or passing it to the media.
"This issue affects a certain subset of loyal workers, who use a very different language and have very different feeling towards it than workers who are temporary," said Organise lead campaigner Usman Mohammed.
"Amazon workers keep telling us that no-one at Amazon asked them about removing the shares, it's why they voted to take their message directly to Jeff Bezos."
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The Amazon CEO's email address is widely available, and Bezos is known to read even customer complaints, sometimes forwarding them to subordinates with a single question mark.
A manager receiving one of these notorious emails has to drop everything to respond as quickly as possible to the request - with no excuses accepted.