"Arsenal Football Club is extremely disappointed by the publication of these false claims which are without foundation," a club statement read.
"The Sunday Times knows that these allegations are baseless but has preferred to publish regardless. The club takes its responsibilities in this area very seriously and our players are well aware of what is expected. We strictly adhere to all guidelines set by the World Anti-Doping Agency [WADA]."
"The claims The Sunday Times put to us are false and entirely without foundation," Chelsea's statement read. "Chelsea Football Club has never used the services of Dr Bonar and has no knowledge or record of any of our players having been treated by him or using his services.
"We take the issue of performance enhancing drugs in sport extremely seriously and comply fully with all anti-doping rules and regulations. Chelsea FC players are regularly and rigorously tested by the relevant authorities."
The evidence was given to the newspaper by a whistle-blower - a former athlete who himself was banned for taking performance enhancing substances. He had initially tipped off United Kingdom Anti-Doping (UKAD) in the hope of receiving a reduced suspension but the authorities dismissed his claims as being of "little or no value".
Bonar has also replied to the report, stating that he never had any relationship with any of the clubs named or their players.
However, to undercover reporters, the 38-year-old did claim to have provided sports people with the blood booster EPO, along with steroids and human growth hormone. Bonar allegedly gained introductions to a host of sports stars through a former Chelsea fitness coach who also reportedly recommended visits to his London clinic to at least one footballer.
Rob Brinded, the fitness coach in question, also sensationally claimed that Chelsea players were involved in taking banned medication during the period 2001-2007. His lawyer later told the Sunday Times those claims had been a "misunderstanding".
The initial reaction to the story came with the sense that there was a storm brewing; that it was football's turn to be put under the microscope following the raids and investigations which have come out in other sports.
The Festina affair, which exploded during the 1998 Tour de France, detailed the prevalence of performance enhancing substances in cycling. The BALCO scandal in 2003 provided evidence of systematic doping in baseball, athletics and other sports. That investigation eventually led to the downfall of Marion Jones, the now-disgraced American sprinter.
Football has not - yet - had a Festina or a BALCO but it is something acknowledged by top medics as being integral to detection of doping in sport.
"While investigations as the primary means of proving doping violations are uncommon in sport, investigations have been successful in highlighting doping practises and developing novel approaches in the fight against doping in sport," Fifa medical chief Professor Dr Jiri Dvorak has written in the British Journal of Sports Medicine (BJSM).
It wasn't merely positive tests that brought down Lance Armstrong or Marion Jones, it was whistle-blowing, reporting and investigating.
If the dope bomb were to go off in football, it would not be detonated by the odd positive test here and there. It would begin with a former player or coach or another kind of whistle-blower. Testing alone will never be enough. Current levels are not up to standard on a number of counts.
Sir Craig Reedie, the president of WADA, called on broadcasters and sponsors to help fund clean sport during his opening speech at last month's annual WADA Symposium for Anti-Doping Organisations in Lausanne.
Amid bumper revenues for football’s top teams due to mammoth television and sponsorship deals - including a new £5.1bn domestic Premier League television contract - Reedie has pleaded for more assistance in the fight against doping. WADA’s annual budget is set at around $26m, about the same amount that Sky Sports will pay to broadcast just two Premier League matches in the UK from next season.
That budget is inadequate for one sport let alone the entire sporting world.
The most recent WADA testing figures from 2014 show that a total of 674 anabolic steroid tests were conducted in football across the year, with only three showing up prohibited substances.
Likewise tests for EPO, human growth hormone and blood transfusions fall similarly short with positive rates close to zero.
Urine tests for erythropoiesis-stimulating agents (ESAs), which stimulate red blood cell production, were conducted in football 2,539 times in 2014. Blood tests for the same were done 493 times with 315 of those coming out of competition.
None were reported as Adverse Analytical Findings (AAFs) requiring a follow up. That's not good. It means either no players in football are blood doping or that the authorities cannot find one.
Tests for Haemoglobin-based oxygen carriers (replacement blood) were conducted 170 times in competition in football as a whole and 15 times out of competition. Homologous blood transfusions were tested for 104 times in competition and 11 times out of competition. No AAFs.
Steroids account for about 60 per cent of football's AAFs but recreational drug users are still statistically more likely to be sanctioned than dopers.
There are over 65,000 professional footballers in the world and all are theoretically eligible to be tested. Potential steroid dopers have barely a one per cent chance of being tested let alone delivering an AAF.
Look closer at the 2014 WADA figures and you will see the gaps. The Brazilian football federation (CBF) - not one blood test in 2014. The same story for Turkey, Portugal, Japan, Netherlands, Russia, Greece, Sweden, Mexico, China, Switzerland, the AFC, Conmebol and Caf.
Sure, Uefa managed to catch the Dinamo Zagreb midfielder Arijan Ademi last year. Can anyone really say that he is the only player with prohibited substances in his system in this season's Champions League? Is testing now so laser sharp that Uefa has managed to catch the one guy breaking the rules?
Dvorak in the BJSM admitted there is an "urgent need" to change detection strategies in football. The number of doping tests in the sport between 2005 and 2012 increased roughly by 50 per cent but the number of AAFs remain much the same.
The message being pedalled by clubs and governing bodies to the public is very different to the message behind the scenes.