For more than 150 years, the logo has been a picture of a dead lion being swarmed by bees, a reference to the biblical story Samson from the Old Testament.
After Samson killed an aggressive lion, he noticed bees had formed a comb of honey in the carcass. He later turned this into a riddle: 'Out of the eater come forth meat and out of the strong came forth honey.'
Lyle's Golden Syrup used the second half of the phrase on the original branding for the golden syrup.
However, the modern branding now shows a lion's face up close with a single bee and it has removed the religious quote.
The Church of England has now criticised the modern rebrand and questioned whether there is 'any place' for Christians in the UK.
Sam Margrave, a member of the General Synod, the Church of England's legislative body, told the Telegraph: 'There is nothing modern about ditching tradition or sidelining Christian messaging.
'I am sure the Lyle business doesn't mind benefiting from sales and Christian branding every Easter, so why do they feel the need to eradicate their connection with their Christian founder's iconic logo which tells a story that works for every generation?
'It does lead to the question, is there a place for Christians or Christian messaging in the UK anymore?'
Mr Margrave added that he hopes that Lyle's Golden Syrupwill 'rethink' the new logo.
Andrea Williams, chief executive of Christian Concern told the newspaper that the company had 'traded the enduring appeal of their brand for a momentary fad'.
The brand has apologised for any upset caused by the switch and is adamant that religion played 'no part' in the move.
Gerald Mason, Senior Vice President of Tate & Lyle Sugars told the outlet: 'Religion played absolutely no part in our decision to try something different on our syrup bottles - a product format where we regularly use different approaches to our brands.
'It makes me sad that we might have unwittingly upset people today, and I want to apologise for that.'
Abram Lyle had strong religious views, which is the reason why the logo depicts the story of Samson from the Old Testament.
The rebrand will take place across the full product range, excluding the classic Lyle’s Golden Syrup tin, which will retain its heritage packaging.
The iconic green tin and golden lion logo holds the Guinness World Record for the world's oldest unchanged brand packaging. The company has had the branding since 1883.
The update will be rolled out to products this month and will continue throughout the year across retail and food service packs, including full-sized bottles, breakfast bottles, dessert toppings and golden syrup portions.
Lyle's Golden Syrup previously hit back at criticism over its modern-day shift, adding that will 'refresh the brand's legacy to appeal to a 21st century audience' and help it to become a product regular on the family breakfast table.
James Whiteley, Brand Director for Lyle's Golden Syrup, said: 'While we'll continue to honour our original branding with the heritage tin, consumers need to see brands moving with the times and meeting their current needs.
'Our fresh, contemporary design brings Lyle's into the modern day, appealing to the everyday British household while still feeling nostalgic and authentically Lyle's.
'We're confident that the fresh new design will make it easier for consumers to discover Lyle's as an affordable, everyday treat, while reestablishing the brand as the go-to syrup brand for the modern UK family, featuring the same delicious taste that makes you feel Absolutely Golden.'
The product has been used in flapjacks, rocky road and sponge puddings since the Victorian era.
Robert Bargery, Executive Director of the Royal Fine Art Commission Trust, told MailOnline: 'A successful brand with a solid reputation probably has more to lose than gain by going for a new logo.
'The redrawn lion is so stylised as to lack clarity at first glance, whereas the old lion is clearly a lion: it is what it looks like on the tin.
'But who knows, Golden Syrup may soon be as stigmatised as cigarettes, so the lively re-brand of a dead lion may excite a sugar-rush among the avocado-on-toast generation.'