Very good question.... I would say using natural materials and choosing shapes and designs that are inspired from nature. Timber is the material that comes to mind.Look at this example of a tree-like structure:
A common approach is to cover a building with a green roof and giving it organic shape. But this is, I believe, a rather blunt way to attempt to make a building look like it is "part" of nature.
(Again) Frank Lloyd Wright considered the building and site to be a whole. He used to look for patterns, materials and colors in the surrounding nature, and found inspiration from these. He then used these as a "grammar" which would then be used in the entire building, from the overall plan to the smallest details. This is quite similar to the fractal patterns we find in nature.
Perhaps, also the building could function like it is part of nature as well as looking like it is part of nature, to form a whole - biomimicry principles like those described by J. Benyus, or the principles of the Living Building Challenge may be useful in this context.
Designing buildings, so they will look like they are part form nature is related to traditional construction methods or what we call now "Vernacular architecture". You might find good examples of what you are looking for in:
. Bernard Rudofsky (1964) “Architecture Without Architects: A Short Introduction to Non-pedigreed Architecture”, A book based on the “NYC MoMA exhibition” (in New York, USA) of the same name. (available at: https://www.moma.org/documents/moma_catalogue_3459_300062280.pdf) . You might see examples of such buildings in a dry climate from simple stone walls used for grape vine plantations in the island of Lanzarote, in Spain (p. 29), to complex structures such as the tower of Samarra in Iraq (p. 119), or the beautiful dome of the bath in Iznic in Turkey (p. 153).
. Paul Oliver (10997) "Encyclopedia of Vernacular Architecture of the World", in 3 impressive volumes.
If you read French (or have someone that might help you) there is a book that might be interesting: "Architectures et nature, 18 exemples internationaux" (1980), sous la direction de Maria Schofield ; traduit de l'anglais par Nicole Vallée; Editeur(s) : Paris : Éds. du Moniteur, 1980 . As contents ( Sommaire) :
P. 2. Le musée d'Art contemporain de Téhéran, Iran
P. 10. La résidence Azuma à Osaka, Japon
P. 16. Une maison dans les pins en Toscane, Italie
P. 22. Maisons-dunes jumelles à Atlantic Beach, Floride, Etats-Unis
P. 28. La maison de vacances de l'architecte à Blokhus, Jutland, Danemark
P. 34. La ville "K" sur le lac Yamanaka, préfecture de Yamanashi, Japon
P. 44. La maison "hot-dog" à Harvard, Illinois, Etats-Unis
P. 50. le musée international d'Horlogerie à La Chaux-de-Fonds, Suisse
P. 60. le café Ingot à Kitakyushu, Japon
P. 66. Une maison solaire près d'Alburquerque, Nouveau-Mexique, Etats-Unis
P. 74. La maison Hopkins, Hampstead, Londres, Grande-Bretagne
P. 82. La maison de l'architecte près de Los Angeles, Californie, Etats-Unis
P. 90. Un appartement à Milan, Italie
P. 94. Une maison sur le lac Washington, près de seattle, Etats-Unis
P. 102. La Fondation Vasarely, près d'Aix-en-Provence, France
P. 110. La résidence Takahara à Tokyo, Japon
P. 116. La casa Vittoria : une maison de vacances à Pantelleria, Italie
P. 122. Le Temppeliaukio à Helsinki, Finlande
You might find images of this book in internet. The foto in its front cover, from a house near the sea, is looking like "it is part of the nature" (sand dunes near the Baltic sea): the Claus Bonderup's Vacation House, Blokhus, in Jutland, Denmark.
That's the whole concept of Bionics... However, getting ideas on possible designs largely depends on the individual's sense of curiosity and observation of the world around and also some eureka moments of inspiration...