Directors of the world-class attraction applied to build several large structures to expand its operations and house species, while the existing, ageing glasshouse is modernised.
City planners did not accept proposals to construct a 200ft-long vehicle garage or plans for extra street lighting, which homeowners said would have impacted on the conservation area.
Local residents, however, said they were worried that the decision paved the way for future “industrialisation” of the park, which could ruin one of the capital’s most treasured green spaces.
Ian Hooper, from the Inverleith Society, said: “Nobody is saying there shouldn’t be any development, but we want to see a long-term plan from the Botanics which would give everyone some assurance of how things are going to happen over the next few years.
“This is a conservation area and we really ought to be able to find a better solution that would respect the character of this area.”
He added: “The decision to remove the vehicle shed, though, is very welcome, because it would have been very visually intrusive”.
Professor Stephen Blackmore, Regius Keeper at the Royal Botanic Garden Edinburgh, said: “This is the first major milestone in a journey which will transform our facilities to match the world-class research work we carry out.”