The court heard of evidence Perepilichnyy had received threats by phone from an organised crime group and had taken out "multiple" life insurance policies before his death.
Bob Moxon Browne, QC, for Legal and General, queried why no one appeared to have asked Perepilichnyy's widow what he had for lunch that day.
He said: "The contents of Mr Perepilichnyy's stomach were flushed away very shortly after his death. There is no bag of stomach contents. There is a quantity of material that was subsequently retrieved from the stomach cavity."
Tests had shown a "suspect compound" that matched the atomic weight of a "vegetable poison", he said.
Moxon Browne said: "This is a case where Mr Perepilichnyy died of natural causes or he was murdered, and if he was murdered it does seem very likely he was poisoned as opposed to any other method of bringing about his death.
"What we are talking about is a vegetable poison as opposed to being irradiated, or heavy metal or something."
The hearing was told of a "rumour" Perepilichnyy had eaten a popular Russian soup containing sorrel during a lunch with his family hours before he collapsed on November 10, 2012.
Tests did not identify the herb in his stomach contents however.
Moxon Browne said the examination was either "not fit for purpose" or there was a "possibility somebody had substituted another vegetable matter for sorrel".
Moxon Browne also indicated there was telephone evidence "about threats from an organised crime group" as he called for police witnesses to give evidence at the full inquest and questioned why of the two phones Perepilichnyy had on him at the time of his death, only one was interrogated.
He added: "If Mr Perepilichnyy was not murdered, then it must have been one of these very rare genetic heart problems."
However Fiona Barton QC, representing Surrey Police, said there is no proof poison played any part in Perepilichnyy's death.
She said: "Two autopsies have been carried out, the second specifically referred to whether he had been killed and, if so, the method of administration,' she said.
"Following those autopsies, numerous samples were taken and subjected to analysis by experts of many disciplines.
"No identifiable toxin was found and that remains the case.
"Even now, not one expert is able to say on the balance of probability, that a toxin is in fact present in Mr Perepilichnyy's body at the time of his death, what that toxin is, how it was administered, what the quantity required would be and how quickly it would take effect."
The inquest into Perepilichnyy's death opened in 2014, but has been hit by a string of delays and the Surrey coroner, Richard Travers, stepped down after a High Court order prevented the disclosure of secret documents.
The full hearing, lasting up to four weeks, will now take place in June before the Recorder of London, Judge Nicholas Hilliard QC.
