Morrisons has decided that they will be rationing the sale of peppers, as they limit customers to buying two packs per person.
The Mirror reports that other stores, such as Waitrose, have reported that stock is running low, as shelves end up empty.
The short supply is believed to be due to poor weather in Spain now and earlier in the year.
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Recently, customers were warned that limits of some fruit and vegetables could drag on until May in most stores.
Tesco and Aldi were among the supermarkets to limit peppers earlier this year. Farmers also warned supermarkets that they were not being paid enough to grow supplies, which further impacted the number of products grown.
Tomatoes were also affected by the poor weather in Spain, which also affected the supply of products from Morocco.
In February, Lee Stiles, secretary of the Lea Valley Growers Association (LVGA), told the BBC: "The majority of tomatoes, peppers and aubergines are not going to be around in big volumes until May."
In the same month, a sign was left out in one Morrisons shop that read: "Availability across our tomato range has been significantly impacted by adverse weather conditions across Spain and Morocco.
"The current shortage is likely to improve within a couple of weeks."
Other shortages include toilet paper, as one business owner warned that a new EU ban on products is linked to deforestation.
Cheeky Panda owner Chris Forbes said to The Grocer: "There will definitely be a squeeze on availability and we can expect the price of recycled tissue to rise as demand for alternatives increases."
Chris said that businesses that are reliant on virgin pulp - which helps to make items like paper towels, facial tissues and toilet paper- as raw material will struggle to make the changes in time.
The company, which produces toilet rolls under the Velvet, Cushelle and Tork brands, said: "Essity fully supports any legislation designed to combat deforestation.
"We have a long history of working closely with our suppliers under strict requirements to ensure that all of our raw materials are sourced ethically and responsibly."
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