Unfortunately, if there is any combination of relatively harmless chemicals that become toxic when mixed in-vivo, then they are either undocumented or classified.
The challenge in a multi-part toxin is in finding precursor compounds that are either non- or minimally- toxic in themselves, and yet are capable of reacting in-vivo to produce a highly toxic compound, without first being altered by the body's metabolism to the point where the desired reaction to produce the highly toxic substance cannot take place.
This is challenging enough, but to add the complication that the precursor compounds must be something that a human would unknowingly ingest reduces the possibilities even further, since many of the potential precursor chemicals could have an unpleasant or at least obvious taste and/or smell.
There are rumours that a viable binary poison is being developed, but these are unsubstantiated.
However, a potential avenue for producing a binary toxin would be to create a toxic compound composed of two proteins that are individually harmless, yet can combine in-vivo to produce a toxic compound. Botulinum toxin is such a two-part toxin. If the two proteins that combine to produce this toxin were produced separately, and then administered separately, the potential exists for them to combine in-vivo and then produce their toxic effects.
However, the two proteins involved would have to be administered separately in quantities much greater than that required for the compounded toxin in order to have the same toxic effect. Additionally, the proteins involved would be denatured by cooking, thus requiring that they be protected from high temperatures prior to administering them to the victim. Finally, it is unknown if these two proteins would survive for as great an amount of time in-vivo when separate (since they would both be exposing surfaces of the folded protein not normally exposed due to their bonding to one-another in normal usage) as when administered in combination, whether an immune reaction may become possible when administered separately, or if the two proteins will actually combine in-vivo to produce their toxic form.
Thus, while it may be simple to say, "Administer the two botulinum toxin proteins separately", there are many potential complications that may render this approach ineffective. However, the potential exists that modified versions of these proteins or other bacterial binary toxin proteins might prove harmless when administered alone, but combine in-vivo to produce toxic effects.