It’s already been established, or at the very least hinted at, that the Infinity Stones were merely the by-products of six entities being destroyed by The Big Bang. During the reveal of The Orb being the Power Stone in Guardians of the Galaxy, The Collector regales the titular group with tales of the what their boon actually is.
There isn't anything more to the story at the moment, though knowing the history of the MCU there will be. For now though there are theories as to a deeper origin to the Infinity Stones. One of which is that they were crafted from the old universe by the Celestials.
Within the comics the Celestials were split into two groups, both of which sprung from the First Firmament (the cosmic manifestation of the first universe) when it got lonely and wanted to make life. The first were known as the Aspirants, who wanted nothing more to appease the First Firmament, whilst the multi-coloured Celestials rebelled and wanted to make their own universes.
We've only seen two Celestials in the MCU so far; the previously mentioned Eson the Searcher and Ego, Star-Lord’s dad. Both of these have seemed to be more of the rebellious lot, what with their selfish desires (whether it’s been destroying stuff or making every life-form like them) so the theory runs that the Aspirant variations are also still around too, trying to honour the First Firmament by holding onto something from the original universe; i.e. by making the Infinity Stones.