From April this year, the quality assurance mark's 45,000 growers and farmers will implement standards that are aligned across all farm sectors for the first time.
An AFS representative said many schemes had developed separately during the 1990s, which had led to differences in terminology, layout and content.
This project brings these differences into line with standards on crops and produce, which have already been better aligned.
All growers in the scheme will receive tailored manuals to help them meet the standards.
The new requirements will be effective for farm inspections from 1 April. As part of the new approach, the AFS has also rebranded the current standards as Red Tractor Farm Assurance.
Describing the importance of the move, AFS chief executive David Clarke said: "It is essential that all sector standards include the same core values."
NFU president Peter Kendall added: "The alignment of farm standards, along with new funding from the Agriculture and Horticulture Development Board, will help to achieve clearer messages about the quality and standards of production by our committed farmers and growers.
"It is vital that our agricultural and horticultural products, which are produced to high, independently inspected standards, are distinguishable in the marketplace."
The AFS stressed that most changes brought in under the plans were a "reflection of recognised good farming practices" and insisted that producers "should have no difficulties achieving them".
A detailed "road map" is being developed to help growers identify the old standards within the new manual. Growers can also check online to see whether any of the updates might affect them (www.assuredproduce.co.uk).
The British Independent Fruit Growers Association has spent the past few years campaigning to reduce the administrative burden placed on growers by farm assurance schemes. Chairman John Breach said this harmonisation will not make life any easier for top fruit growers.
"We are still not happy with these farm assurance schemes," he complained.
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