The drawing of pictures in manuscripts is known as Illumination*
The Wikipedia article on the subject (as mentioned in a previous answer) contains a wealth of information on the subject, including this gif showing the steps:
Image from Wikimedia commons: link
Steps involved (from the image caption):
- I. Graphite powder dots create the outline
- II. Silverpoint drawings are sketched (you could use pencil instead here)
- III. Illustration is retraced with ink
- IV. The surface is prepared for the application of gold leaf
- V. Gold leaf is laid down
- VI. Gold leaf is burnished to make it glossy and reflective
- VII. Decorative impressions are made to adhere the leaf
- VIII. Base colors are applied
- IX. Darker tones are used to give volume
- X. Further details are drawn
- XI. Lighter colors are used to add particulars
- XII. Ink borders are traced to finalize the illumination
This is the technique used in illumination.
As for the materials, despite your misgivings tempera is actually extremely robust and was used for all miniatures, along with ink and gold/silver leaf. Tempera's resistance should be obvious from the fact that we have many surviving tempera paintings that are hundreds or even thousands of years old.
Tempera can't be stored, but it's easy to make yourself with egg, water and pigment.
The Wikipedia article also contains a list of common pigments used in Medieval times - you can try your hand at making these, or use easily available synthetic pigments.
As a final aside, vellum is expensive and relatively rare these days but it is still available.
*In the strictest sense illumination refers only to pictures containing gold, but in normal usage it covers all drawings of this type.