This answer only provides a rough outline, as I do not possess comprehensive knowledge of the history of European mathematics, let alone the global history of mathematics. The gist of the development process seems to have been be that square roots were exclusively positive for three millenia, then the square root began to be considered as a multi-valued operation for several centuries, until we mostly focused back on the principal branch at some time during the 20th century.
The Babylonian clay tablet YBC 7289 dated to about 1700 B.C. provides the first known evidence of a square root computation, giving $\sqrt{2}$ to three sexagesimal places: $1;24,51,10$. The exact process by which this result was computed is not known. The Greeks likely learned of square roots from the Babylonians. Hippasus of Metapontum (5th century B.C.) is credited with proving that $\sqrt{2}$ is irrational. Book X of Euclid's Elements (3rd century B.C.) demonstrates how to manipulate expressions involving square roots, although on a purely geometric basis. In the 1st century A.D. Heron of Alexandria gave a numerical method for computing square roots, likely of much older origin. Up to this point there was no notion of negative numbers in mathematics, thus all square roots were positive by default.
The Chinese book The Nine Chapters on the Mathematical Art from the 1st century A.D. contains the first known appearance of negative numbers, a concept further developed by the Chinese mathematician Liu Hui in the 3rd century. But it would be a long time before the concept was introduced into European mathematics. The 15th century French mathematician Nicholas Chuquet is credited with the first use of negative numbers, limited to exponents only [4].
From what I could find, Simon Stevin's L'Arithmetique (1585), contains the first examples of negative roots in the history of European mathematics, in the context of quadratic equations. One example is found in article II on p. 333, where he shows that $x^{2}=4x+21$ has a solution $-3$. The first direct presentation of the square root as a multi-valued operation that I could locate is in Colin MacLaurin's A Treatise of Algebra, published posthumously in 1748. On p. 43:
It appears from what was said of Involution, that "any Power that has a positive Sign may have either a positive or negative Root, if the Root is denominated by any even Number." Thus the square Root of $+a^{2}$ may be $+a$ or $−a$, because $+a \times +a$ or $−a \times −a$ gives $+a^{2}$ for the Product.
It should be noted that Indian mathematics had reached the equivalent notion by the 12th century. Henry Thomas Colebrooke (tr.), Algebra, with Arithmetic and mensuration, from the Sanscrit of Brahmegupta and Bháscara. London: John Murray 1817, p. 135 quotes from the Bījagaṇita (Algebra) of Bhāskara II (c. 1114-1185) as follows:
The square of an affirmative or of a negative quantity is affirmative; and the root of an affirmative quantity is two-fold, positive and negative. There is no square-root of a negative quantity: for it is not a square.
I was able to trace the presentation of the square root as a multi-valued operation through German textbooks [1,2,3] from 1768 right to the end of the 19th century, which suggests that this was a commonly and consistently held notion. J. Brunotte, Lehrbuch der Arithmetik und Algebra für Gymnasien, Real- und Handelsschulen. Nürnberg 1894, p. 78:
Da sowohl $(+a)^{2}=a^{2}$ als auch $(-a)^{2}=a^{2}$, so folgt $$\sqrt{a^2}=\begin{cases} +a \\ -a \end{cases} \ \ \text{ ebenso } \sqrt{4}=\begin{cases} +2 \\ -2 \end{cases} \ \ \ \ \sqrt{\frac{64a^{4}}{49x^{2}}} = \pm \frac{8a^{2}}{7x} $$
d.h. jede Quadratwurzel gibt zwei, nur dem Vorzeichen nach entgegengesetzte Werte, ist also im allgemeinen zweideutig. In den folgenden Untersuchungen und Rechnungen werden jedoch nur die absoluten Werte in Betracht gezogen werden.
This notes that the square root operation is multi-valued, but advises the reader that the further text will consider the absolute values only.
Google Books does not constitute a good source for literature past the 1920s, presumably due to copyright issues, so I have had no luck in tracing the presentation of the square root in textbooks for middle schools or high schools any further. I do not recall what happened in my own math classes, but located among my books one widely used mathematical textbook from Germany (Lambacher-Schweizer) from 1981, where the "Quadratwurzelfunktion" (square root function) is defined as $\mathbb{R}_{0}^{+} \mapsto \mathbb{R}_{0}^{+}$, that is, covering the principal branch only.
Some commenters under this question have opined that the focus back on the principal branch was a consequence of the introduction of electronic calculators and programming languages for computers (in particular since about 1970) whose $\sqrt{}$ keys and sqrt() math library functions are limited to that. I consider that plausible, but not conclusive evidence.
[1] Heinrich Wilhelm Klemm, Mathematisches Lehrbuch. Stuttgart 1768, p. 127: "Eine jede quadratische Gleichung hat 2 Wurzeln, dann von $x^{2}$ kann $+x$ und $−x$ die Wurzel seyn."
[2] Joseph Melchior Danzer, Mathematisches Lehrbuch. Erster Teil. Munich 1781, p. 66: "Alle Wurzeln von geraden Exponenten können also zweyerley seyn, positiv und negativ. $\sqrt{9}=\pm 3$. Die Wurzeln von ungeraden Exponenten aber haben nur das Zeichen, welches ihre Würde hat. Z.B. $\sqrt[3]{−8}=−2$."
[3] Franz Minsinger, Lehrbuch der Arithmetic und Algebra. Augsburg 1832, p. 100: "Das Ausziehen der Quadratwurzel aus Zahlen (ganzen, gemischten und gebrochenen) ist bekanntlich das Zerfällen der gegebenen Zahlen in zwei gleiche Faktoren, daher die gegebene Zahl stets positiv sein muß, die Wurzel aber positiv und negativ sein kann. [...] z.B. $\sqrt{81}=\pm 9$
[4] Chuquet used $\bar{\mathrm{p}}.$ for $+$ and $\bar{\mathrm{m}}.$ for $-$. One of his examples is the multiplication of $8^{3}$ by $7^{1 \bar{\mathrm{m}}.}$ resulting in $56^{2}$, meaning (I think) $8x^{3} \cdot 7x^{-1} = 56x^{2}$.